A Functional Medicine Evaluation in a Child with Autism

Your son has not pooped in four days. He is up at 2 a.m. most nights. He eats six foods, and one of them stopped being acceptable last month. Since March he has had three rounds of antibiotics.

Those are real problems. Every one of them is measurable. Every one of them is worth attention on its own, whoever your child is.

Here is exactly what I look at in a child with autism, and here is the list of things I will not tell you.

What do parents ask me most about this?

Short answers first. The full reasoning is below.

What does a functional medicine evaluation look at in a child with autism?

A functional medicine evaluation in a child with autism looks at five ordinary medical things. Bowels. Sleep. Feeding and nutrient status.

What will this evaluation not do?

This evaluation will not change who your child is, and it is not an autism therapy. Autism is not a disease.

Why do I start with constipation and daily stooling?

I start with constipation because it is common, because it is measurable at home, and because it hurts.

Why does sleep get looked at so early?

Sleep gets looked at early because it is one of the most common problems that comes along with autism, and one of the most worth working on.

What does feeding difficulty do to a child's nutrient status?

Feeding difficulty narrows what goes in, and a narrow diet can leave real gaps. A meta-analysis of 17 studies found children with autism experienced significantly more feeding problems than their peers, with an odds ratio…

Which labs do I check in a child with autism?

I check ferritin with iron studies, 25-OH vitamin D, a full thyroid panel, zinc and copper as a ratio, and lead.

What would each finding mean, and what would it not mean?

Each finding in this evaluation means one thing and not another. A low ferritin means a child needs iron, not that iron explains his autism.

Why do recurrent infections matter in this evaluation?

Recurrent infections matter because a child who has had several courses of antibiotics in a year is a child whose immune system and gut have both been working hard.

What does a functional medicine evaluation look at in a child with autism?

A functional medicine evaluation in a child with autism looks at five ordinary medical things. Bowels. Sleep. Feeding and nutrient status. Recurrent infection. And discomfort or pain that nobody has located yet. Each one is a real medical issue. Each one is measurable. Each one is worth addressing in its own right.

Autism is not on that list. That is deliberate. I am looking at the load a child is carrying, not at who he is.

A child who is constipated and not sleeping is a child under load. That is true of any child. It does not become a different statement because he is autism, and it does not become less urgent because everyone around him has stopped asking medical questions and started asking behavior questions.

What will this evaluation not do?

This evaluation will not change who your child is, and it is not an autism therapy. Autism is not a disease. I do not offer recovery, reversal, healing or a return to some other version of your son. Nothing on my list will make him not autism, and I would not want it to.

I want to be more specific than that, because vagueness in this lane is how families get hurt.

I will not tell you that a supplement, a diet, a stool test or a genomic panel changes autism. I will not show you a before-and-after child. I will not describe a child's autism traits as damage, and I will not describe your son as recovering. I will not promise that helping his constipation will change his diagnosis, because it will not. I will not sell you a protocol built on the idea that your child is broken.

There is a real market that does all of those things. In 2015 the Federal Trade Commission settled charges against a company selling children's supplements, with a $3.68 million judgment, most of it suspended, over claims about children's speech and about communication and behavior in children on the autism spectrum.8 If you have felt uneasy reading a supplement page about autism, your instinct was correct.

What I will tell you is narrower and, I think, more useful. If your son is constipated, I will work on the constipation. If he is not sleeping, I will work on sleep. If his ferritin is low, I will correct the ferritin. Those are worth doing for their own sake, for any child, and I will say exactly that and nothing more.

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Why do I start with constipation and daily stooling?

I start with constipation because it is common, because it is measurable at home, and because it hurts. A meta-analysis of studies comparing children with autism with other children found higher rates of gastrointestinal symptoms overall, and specifically higher rates of constipation, diarrhea and abdominal pain.2 Constipation is not a behavior. It is a plumbing problem with a behavior shadow.

The shadow is worth understanding. In a study of 176 children with autism aged 2 to 7, more than nine in ten had at least one gastrointestinal symptom, and constipation was among the most commonly reported.3 In that same study, gastrointestinal symptom severity tracked with repetitive behaviors and with irritability.

I want to be careful about which direction that arrow points, because nobody actually knows. An association is not a cause. What I can say is that a child in abdominal pain who cannot explain abdominal pain will show you something else instead, and that is true of every child on earth.

So daily, soft, complete stools come first. Not because it changes his diagnosis. Because it is uncomfortable to be that backed up, and because I cannot read anything else clearly until it is handled. When simple measures have not been enough, pediatric gut and microbiome testing is how I look at what is going on underneath.

Why does sleep get looked at so early?

Sleep gets looked at early because it is one of the most common problems that comes along with autism, and one of the most worth working on. In an autism registry study of 1,518 children aged 4 to 10, 71 percent scored in the range associated with clinically significant sleep problems on a standard parent questionnaire, while only 30 percent had a sleep diagnosis on record.4

Read those two numbers next to each other. That gap is the whole reason I ask about sleep in detail, in the parent's words, rather than checking a box. Parent concerns about sleep often do not make it into the clinic note.

The same study found that children taking medications for sleep had worse daytime behavior and lower quality of life than children who were not.4 That is not proof the medications caused it, and the authors do not claim it is. It is a reason to look at what is keeping a child awake before reaching for something to make him sleep.

In practice, the children I see who are up at 2 a.m. are often uncomfortable, hungry, itchy, congested, or in pain. Sometimes it is none of those and it is simply a body clock that needs help. Either way it is worth working out, and that work happens in a pediatric sleep support consult.

What does feeding difficulty do to a child's nutrient status?

Feeding difficulty narrows what goes in, and a narrow diet can leave real gaps. A meta-analysis of 17 studies found children with autism experienced significantly more feeding problems than their peers, with an odds ratio of about 5, and lower intake of calcium and protein.5 That is a nutrition question, not a behavior question.

This is where I am most likely to find something I can actually correct. It is also where I most want to protect a child from a bad idea. A restrictive diet layered on top of an already restricted diet is not a plan, it is a risk. Quality matters more than a long list of nevers, and what is right for one child is not right for the next.

Six foods is not a moral failure and it is not something you caused. It is information about sensory experience, gut comfort, or both.

Which labs do I check in a child with autism?

I check ferritin with iron studies, 25-OH vitamin D, a full thyroid panel, zinc and copper as a ratio, and lead. Those are ordinary pediatric labs. I check them because a child with a narrow diet has a real reason to be low in something, and because low numbers are correctable.

Here I have to give you the honest version of the iron literature. A US study of 222 children with autism measured serum ferritin and iron studies and found 8 percent with low ferritin, but the authors concluded their data did not support the idea that children with autism are at greater risk of iron deficiency than other children.6 They also noted their estimate may be low, because ferritin rises with inflammation and they had no inflammation marker.

So I do not check ferritin because your son is autism. I check it because he eats six foods, and because 8 percent is not zero, and because a low ferritin makes any child feel worse. That is the honest reason, and it is a good enough one.

The American Academy of Pediatrics clinical report on autism is clear that co-occurring medical conditions are common and deserve evaluation and management in their own right.1 That is the lane I work in. I am not operating outside consensus here. I am spending more time inside it than a 15-minute visit allows.

What would each finding mean, and what would it not mean?

Each finding in this evaluation means one thing and not another. A low ferritin means a child needs iron, not that iron explains his autism. Constipation means his bowels need help, not that his bowels caused his diagnosis. Keeping those two columns separate is the entire discipline of this work.

Bowels

How I look at it: Daily home tracking, and gut testing when simple measures have not worked

What a finding would mean: He is uncomfortable, and that is worth addressing for its own sake

What it would not mean: That his bowels caused his autism, or that helping them changes his diagnosis

Sleep

How I look at it: A detailed sleep history in your words, plus what is happening in his body at night

What a finding would mean: Something is keeping him awake and it can usually be named

What it would not mean: That sleep is the reason he is autism

Feeding and nutrient status

How I look at it: What he actually eats, plus ferritin and iron studies, 25-OH vitamin D, zinc and copper as a ratio, and lead

What a finding would mean: There may be a gap I can correct

What it would not mean: That a supplement changes autism traits

Recurrent infection

How I look at it: History, and conventional blood work for immune function

What a finding would mean: His immune system is under repeated strain and that is worth understanding

What it would not mean: That an infection created his autism

Unlocated pain or discomfort

How I look at it: Careful history, physical exam, and referral to his own doctors when it belongs there

What a finding would mean: Something hurts and he cannot say where

What it would not mean: That behavior is always pain, or that pain explains everything

Why do recurrent infections matter in this evaluation?

Recurrent infections matter because a child who has had several courses of antibiotics in a year is a child whose immune system and gut have both been working hard. I want to know how often, what for, and what happened after each one. That is a history question before it is a testing question.

I am not going to make a bigger claim than that here. Sudden-onset changes after infection are a separate and specific picture with its own criteria, and if that is what you are describing, PANS and PANDAS care is the page that covers it properly rather than in a paragraph.

For most families reading this, the infection question is simpler. Fewer ear infections and fewer courses of antibiotics is a good outcome by itself.

What if my child has already tried a lot of things?

Most families have. A systematic review of 20 studies covering 9,540 participants found the reported use of complementary and alternative approaches in autism ranged from 28 to 95 percent, with a median of about 54 percent, and that special diets and supplements were the most common.7 If you have tried things, you are the majority, not the outlier.

What I usually find is not that families tried the wrong things. It is that they tried nine things in six weeks, and now nobody can say which one did anything. That is not a more thorough plan. It is an uninterpretable one.

So I go slowly and in a specific order, one new thing at a time. I ask you to tell me before you stop anything. And I keep the list short enough that you can actually run it on a Tuesday night when everyone is tired.

You did not cause this. You have been doing the hardest version of this job with the least information, and you have been doing it while white-knuckling through every day.

How does this fit with my child's other providers?

This work sits alongside your child's other care, not instead of it. His pediatrician stays his pediatrician. His developmental team stays his developmental team. Speech, occupational and behavioral therapies are their own field and they are not mine. Referrals come from his primary care provider.

I do not write plans that ask you to stop something another clinician started. Antipsychotics and other psychiatric medications are never stopped abruptly, and any change to them belongs with the prescriber. Seizures go straight to neurology. Bleeding and emergencies go straight to emergency care.

What I add is time and measurement on the medical questions that get squeezed out of a short visit. That role is explained in full on my page about what a natural pediatrician does.

I do not want to look at your child like a diagnosis. Autism traits, sleep issues, headaches, gut symptoms and behavior are all clues, but they do not always tell me why a body is struggling. So I go looking at the body, carefully, and I tell you plainly what I find and what it does not mean.

Your son is not a project. He is not a puzzle to be solved and he is not something to be undone. He is a kid who deserves to poop comfortably, sleep through the night, eat enough of the right things, and not hurt. Those aren't small things. They are most of a childhood.

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Families work with me for pediatric functional medicine in Omaha in person, and by telehealth in Nebraska, Arizona, Colorado, Iowa, Tennessee and Virginia.

Written by Dr. Amy Patton, Founder Happy Kid Functional Medicine

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About the author

This article was written by Dr. Amy Patton, DNP, APRN, CPNP-PC, FMACP, a board-certified pediatric nurse practitioner and functional medicine provider serving Omaha-area families through Happy Kid Functional Medicine. Dr. Patton specializes in root-cause pediatric care for children's gut health, sleep, behavior, nutrition, immune patterns, and whole-child wellness. She sees patients in person in Omaha and by telehealth across Arizona, Colorado, Iowa, Nebraska, Tennessee, and Virginia.

References

1. Hyman SL, Levy SE, Myers SM; Council on Children With Disabilities, Section on Developmental and Behavioral Pediatrics. Identification, evaluation, and management of children with autism spectrum disorder. Pediatrics. 2020;145(1):e20193447. doi:10.1542/peds.2019-3447 PubMed

2. McElhanon BO, McCracken C, Karpen S, Sharp WG. Gastrointestinal symptoms in autism spectrum disorder: a meta-analysis. Pediatrics. 2014;133(5):872–883. doi:10.1542/peds.2013-3995 PubMed

3. Chakraborty P, Carpenter KLH, Major S, Deaver M, Vermeer S, Herold B, et al. Gastrointestinal problems are associated with increased repetitive behaviors but not social communication difficulties in young children with autism spectrum disorders. Autism. 2021;25(2):405–415. doi:10.1177/1362361320959503 PubMed

4. Malow BA, Katz T, Reynolds AM, Shui A, Carno M, Connolly HV, et al. Sleep difficulties and medications in children with autism spectrum disorders: a registry study. Pediatrics. 2016;137(Suppl 2):S98–S104. doi:10.1542/peds.2015-2851H PubMed

5. Sharp WG, Berry RC, McCracken C, Nuhu NN, Marvel E, Saulnier CA, et al. Feeding problems and nutrient intake in children with autism spectrum disorders: a meta-analysis and comprehensive review of the literature. Journal of Autism and Developmental Disorders. 2013;43(9):2159–2173. doi:10.1007/s10803-013-1771-5 PubMed

6. Reynolds A, Krebs NF, Stewart PA, Austin H, Johnson SL, Withrow N, et al. Iron status in children with autism spectrum disorder. Pediatrics. 2012;130(Suppl 2):S154–S159. doi:10.1542/peds.2012-0900M PubMed

7. Höfer J, Hoffmann F, Bachmann C. Use of complementary and alternative medicine in children and adolescents with autism spectrum disorder: a systematic review. Autism. 2017;21(4):387–402. doi:10.1177/1362361316646559 PubMed

8. Federal Trade Commission. Company that touted products' ability to treat children's speech disorders settles FTC charges it deceived consumers. Press release, January 9, 2015. Federal Trade Commission. Case: NourishLife, LLC (FTC File No. 132 3152). source

Medical disclaimer: This article is educational and is not medical advice. It does not diagnose, treat, or replace individualized care from your child's pediatrician or licensed medical provider. Supplement types, doses, and combinations should be selected with a qualified clinician who knows your child's full history — never start a new supplement based on a blog post alone. Always consult your pediatrician before making changes to your child's routine, and seek prompt medical care for snoring with gasping or pauses in breathing during sleep, or for any severe, sudden, or concerning symptom.