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Yup, GAPS can fail. And it’s probably not your fault.

Gut and Psychology Syndrome Diet has a lot success stories, and merits too. But what about the kids who fail on GAPS?

I have met a lot of those kids. After GAPS has just plain not worked (or worse – traumatized the family and injured the child, which can unfortunately happen) – I’m often the next stop.

These are smart people who followed the GAPS protocol carefully, and engaged lots of on line support. Most worked with GAPS certified practitioners (which anyone can become, with an on-line 12 week training).  But still: Fail. Their kids withered on bone broth; vomited, or had bloody stool on probiotic foods; lost weight, stopped growing; and had bloating, rashes, and irritable stools with egg yolks, avocados, and nut butters. Their parents pressed on, for months or even longer. Many moms have described to me the intense pressure they felt to stay with this protocol, and the deep sense of failure they internalized about it not working. For them, GAPS was a cult they didn’t know how to leave. The kids suffer physiologically as well, struggling through the deep restrictions and rules of GAPS.

Here’s the thing: There are gaps in the GAPS diet, for many babies and kids. There is no one diet that works for everyone. After twenty five years in clinical practice as a pediatric nutritionist/dietitian, I have absolutely found this to be true. All children with autism, FPIES, or gut issues do not need or benefit from GAPS. I have met many who failed on it. GAPS works well for some. It fails for others. If it isn’t going well, you aren’t a bad parent. Your child just needs something different.

GAPS aims to create a healthy gut microbiome by starving out disruptive microbes in the gut flora, by giving foods that help the gut tissue repair itself, and by using fermented foods to repopulate with healthy flora. So, what can go wrong? Why not just try it?

Besides the possibility of wasting a lot of money and effort preparing scratch foods that may be wrong for your child, you might waste time too – which some young children, and certainly babies, simply can’t afford. The younger they are, and the more undernourished they are to start, the harder this can be on a child, if it isn’t the right measure.

And a mom’ s worry is no small thing. Chronic, strong apprehension and anxiety about anything is hard on parents. It changes your chemistry, and ups your cortisol. Sensitive children will sense your strain, and this will strain them. If you’re breastfeeding, altered cortisol levels are in your milk too. Cortisol changes blood sugar metabolism and endocrine function; it can disrupt sleep, appetite, feeding, and immune response.  If implementing GAPS (or any special diet measure) is exceedingly stressful, hit the pause button: Relax and enjoy your children. Secure professional guidance so you don’t have to carry the nutrition-flip project on your own shoulders.

Meanwhile, here’s what can go wrong, when GAPS is the wrong tool for the job:

Fungal Failure – Recently an old study jumped out at me. It examined how children in weaker nutrition status can’t control Candida (fungal) species very well. They have more Candida, and different, more irritating strains of Candida in their intestines, compared to children in good nutrition status. The study found that for children, simply being in better total nutrition status meant better control of Candida colonization.


What exactly does this mean?

For kids, nutrition status = growth status. It is the single most potent predictor of how well a child will manage any illness or infection. Being underweight or stunted = immune suppression, more infection, and more mortality for children.

Nutrition status in kids is not a measure of how many vegetables or fermented foods they eat. Not whether they’re gluten free, GAPS, or Paleo. Not what supplements they’re on, not whether they drink raw camel milk. No matter what a child eats, if growth pattern has wandered below that child’s innate and expected trend, all body systems struggle more – especially the immune system. Growth pattern as indicator of nutrition status in children – and as predictor of how children manage infection – has been deeply documented, across the globe, in every culture and locale, for nearly a century. This is nutritional epidemiology.

Even when children eat  lousy processed food, if they are in robust growth status, they still have more reserve to tackle a disruptive biome. Whether it’s a fungal load in gut, mycoplasma in lungs, MARCoNs in nasal passages, covid-strain-du-jour, or a viral story in brain tissue, there is simply more energy and building material around to throw at it, in a kid with a strong growth pattern. This is established nutrition science, and you can read more about this cycle of malnutrition and infection in children here.

This does not mean that the quality of your child’s diet doesn’t matter. But it does mean that even if your child eats beautiful food, once in a weakened growth pattern, they are going to struggle more in every way – sleep, mood, infection fighting, learning, behavior – and, detoxifying a dysbiotic gut biome so they can heal the gut.

In the study mentioned above (from 1974, back when there were no GMOs, and less processed food available than is now fed to children worldwide), the groups compared were well-fed white Australian children, poor aboriginal Australian children, and poor Indonesian children. The underfed children had weak total diets, meaning they had too little protein, too few total calories, insufficient vitamins and minerals, and sparse nourishing fats. They also had more Candida.

What does this have to do with GAPS? Read on to see what I mean by the gaps in GAPS.

A small child’s immune system will sputter when s/he’s underfed – like when eating just broth for more than three weeks (as many moms I’ve spoken with have tried). Or when exclusively breastfed or formula-fed, with no solid foods, past the first year. Or when restricting or eliminating healthy starches and carbs – which are fundamental to steady growth in children. In a lapsed growth status, children don’t have enough protein, energy (calories), and nutrients around to feed demands for building tissue and fighting infection.

GAPS diet uses traditional fats generously, which is fabulous in many ways. But, fats don’t replace starches and carbohydrates for babies and kids. Fats as a macronutrient can’t make up this calorie deficit, as nourishing as fats are in their own right:  When kids eat low carb, high fat, high protein diets, it can cause stunting, as this eating pattern changes how growing bones deposit minerals and protein into their tissue. In fact, diets like GAPS that over-restrict carbs, eg ketogenic diets, have multiple potentially injurious effects on children. Ketogenic diets can be therapeutic for specific situations like epilepsy, and I have used this strategy many times in practice. But it isn’t the only way to a healthy gut biome.

Carbohydrates and starches are demonized in GAPS. When I work with families who have fled GAPS, I find that their children are eating as little as ten percent of their total food intakes as starches or carbs – when kids generally need about half their food intakes to be from starches and carbs! If a child has a deep growth impairment, an even higher percentage may be needed.  Many moms have shared with me how terrified they are to give their children even the healthiest starches, for fear of “hurting them” or “causing yeast”. But the reality is that when we are growing, starches and carbohydrates provide the actual fuel our tissue and especially the brain needs to grow and function. Carbs and starches spare the protein and fats we eat for other critical functions, like building tissue. That process needs fuel, which is what carbs and starches provide during growth.

If an already weak, underweight child attempts GAPS, it may fail, because s/he was too depleted for multiple immune-essential nutrients and energy (calories) in the first place. A more recent study illustrates this well known piece in infant and child nutrition: Just by not having enough food around, the gut barrier is disturbed, and tissue damage occurs. It doesn’t take long for this to happen in young children. Long short, being underweight or in growth failure causes leaky gut. Adding probiotic can hasten recovery, but only when an adequate total diet is also in place.

Hence the susceptibility to Candida – and quite likely, other bad actors in a gut biome, tissues, or organs. So although this first phase of GAPS may clear out some disruptive species from the gut, it can also drop your child’s total body immune response further, and permit other unwanted gut species to flourish. For kids who are underweight or have marginal iron stores to start, or who have heavy background mold or viral burden, this can set up for failure. The detox is too fast, and the re-build fails, because the foundation was too weak to begin with, and because the foods used are not adequate to restore fast enough.

Even mild nutrition deficits impact immune response in children. This is another reason why GAPS can fail. GAPS can be too restrictive for too long to help these kids recover. Just the introduction phase of this diet can take three weeks; this is an eternity for an already underweight toddler struggling at the bottom of the growth chart. Though broths, probiotic foods and egg yolks are nourishing foods, this may not be enough sustenance for a growth-impaired small child whose immune system is already straining.

Carbs are especially essential for children. In infancy and toddlerhood, they are the fermentable food that normal gut flora require to thrive. Healthy gut flora make fatty acids like butyrate, which in turn fuel cells building your child’s gut tissue. I’ve met many parents who fear carbs, and over restrict them in their kids. This can fail too. Non-sugary, unprocessed carbs are a cornerstone to fuel the tutorials going on in a young child’s gut, between gut flora and the developing immune system. They also fuel growth and gain, and protect the lovely fats and proteins needed for other functions. The trick is finding which ones work best for your child’s circumstance. This is something I work with closely in my practice, for each individual child.

So even though GAPS aims to eradicate fungal load by restricting all carbs for a while and by adding extremely high potencies of probiotics with fermented foods, it can backfire. I often see disrupted stool cultures in kids coming off GAPS attempts, showing weak beneficial flora and ample dysbiotic bacteria, and even yeast in some cases.

When Leaky Gut Begets Leaky Gut – Some GAPS mainstay foods – even Stage 1 foods – are renown suspects when it comes to food intolerance or allergy, like egg yolks, eggs, or dairy yogurt. Other foods are high FODMAPs and thus triggering for severe FPIES reactions, like artichoke, avocado, or garlic. Eating broth with probiotic foods for three weeks is not long enough to repair leaky gut tissue in a growth-failed child, or to clear pre-existing food antibodies, which can circulate for months or even years after exposure. If a child starts GAPS with hidden food allergy or sensitivity to egg or nuts, using these daily can exacerbate leaky gut, even when using that beautiful kraut or other probiotic food. I often find strong egg and nut reactions on IgE and/or IgG panels children who have used GAPS for several months. Even yolks can trigger immunoglobulin reactions that may not show on the “drop on wrist” test suggested in the GAPS protocol.


Better move: The “dot on wrist” test may not be enough. Do some food antibody testing before you start any special diet. Identify what foods are safest to work with before you begin. Check for both allergy (IgE) and sensitivity (IgG) to several foods, and work from there. If eggs and nuts light up your child’s panel, GAPS is not for you – or, it will be a bumpier road –  consider easier paths than GAPS to gut healing in this case – there are many options.

FODMAPS Meltdown – Many kids have difficulty with foods that are high in FODMAPs. Another GAPS mainstay, avocado (which is indeed a great food) is a moderate FODMAPs food that is poorly tolerated by many in my practice, especially babies and toddlers with FPIES. I am encountering many FPIES families who turn to GAPS, with poor results (vomiting to shock, blood in stool, lagging growth). Learn why FPIES may be as much about carbohydrate fermentation in the gut than it is about food protein reactions here. Meanwhile, if your child has FPIES, I would hesitate to recommend GAPS, because FPIES reactions can be severe and dangerous. I am seeing success with FPIES in my practice with other strategies to resolve gut dysbiosis, a root cause of FPIES. For one on one help, contact me for an appointment.

Dairy Dilemma – Dairy yogurts are another wonderful food that are simply wrong for some of us. In my house, I can eat dairy while my husband and son cannot. I love raw goat milk. I have occasional organic yogurt binges. I eat ice cream, goat cheddar, sheeps yogurt, and whatever I want. My family can’t. I have countless children in my practice who show clean lab findings for any sort of dairy reaction from opiate (excess casomorphin) formation to IgG, IgE, and other tests – but who still disintegrate terribly on dairy. Usually this is  a “behavioral” reaction – anxiety, impulsivity, rage reactions, stilted social processing, or poor sleep. Sometimes, a meticulous elimination trial is the only way to know if your child really can manage a food.

Are dairy yogurts okay for your child? If you really want to know what is going on, consider doing a Cyrex Array 4 for cross reactivity testing. Your child may react to dairy foods when eaten with other foods, and this panel will find if this is true for you child. This test plus sensitivity and allergy tests (IgG and IgE) can guide you before you begin.

Did GAPS Work For Your Kids? Great! Share your success stories here, I’d love to hear them. If it failed, don’t despair. Get individualized expertise for your child’s gut healing (and thus total body healing) journey. Your child deserves to visibly trend toward thriving. If you’re still struggling, get help, give me a call, set up an appointment. There are many ways to replenish, restore, and heal the gut; it’s okay if every kid is different. Honor your instincts as mom, because they are good as gold.