Identifying Nutrition Gaps with Elimination Diets in EoE

by Kelli Miller, MS, RD, LD

In 2018, while working as a pediatric gastroenterology (GI) dietitian, I noticed my son Cole developing worsening reflux and vomiting around 6 to 9 months of age. At first, I thought it was just reflux, but my experience as a dietitian told me it was something more. After a hospital visit for dehydration, an endoscopy confirmed that Cole had EoE, and we decided to proceed with a 4-food elimination diet (milk, egg, wheat, soy). After 12 weeks of strict elimination, Cole’s endoscopy results were normalized.

The journey wasn’t easy. As an infant, Cole relied heavily on amino acid-based formula (AAF) due to his limited diet. Transitioning to AAF was tough due to its distinct taste, but he eventually adapted. We also faced significant financial strain since our insurance didn’t cover the cost of the formula, specialty foods, and medical expenses.

Today, Cole is thriving at 7 years old, still following his 4-food elimination diet (4-FED) with supplemental AAF to ensure he meets his nutritional needs.

Diet Therapies for EoE

1. Elemental Diet (AAF) using AAF to replace all dietary antigens, has been a highly effective treatment for EoE. It can induce quick remission, with a 2020 study showing nearly 94% of patients achieving histologic remission. However, it can be challenging for older children or those with feeding disorders due to its restrictive nature. The diet can also be costly and emotionally taxing, especially for children who are socially impacted by food restrictions.
2. Empiric Elimination Diet involves removing foods based on clinical experience. Based on the recent 2025 ACG guidelines for EoE, the efficiency ranges of various elimination diets are as follows: dairy-only elimination shows an efficacy of 35-45%, dairy and wheat elimination ranges from 40-45%, 4-FED has an efficacy of 40-50%, and a 6-food elimination diet (6-FED) ranges from 40-70%. The 6-FED removes milk, egg, wheat, soy, nuts, and seafood. While effective, these more restrictive diets come with risks like nutritional deficiencies and the need for repeat endoscopies. Additionally, the emotional toll of restricting food choices, can contribute to disordered eating patterns. Working closely with a dietitian is essential to navigate these challenges.

Identifying and Filling Nutrient Gaps

Key Nutrients in Elimination Diets

A 2019 study explored the major nutrients in the top allergens and protein was shown to be the top nutrient in milk, egg, soy, nuts and seafood. While other protein sources can be used, they may not always be well accepted, and feeding aversions or inflammation from flare-ups can make it difficult to consume adequate protein. Milk is particularly crucial as it is a major allergen in EoE and provides a complete protein with all essential amino acids, along with vital micronutrients like calcium, iron, and vitamin D. Without cow’s milk, many children struggle to meet these needs.

Plant-based milks (PBMs) are a common replacement, but they often lack the protein, fat, and vitamins found in cow’s milk. Soy and pea milks are exceptions but may not be suitable for children with other allergies. PBMs may also contain added sugars, so choosing unsweetened varieties is essential. A 2020 position paper states that when PBMs are used as the primary milk source for older children, their diet should also include alternative sources of protein, calcium, iron, and vitamins B-12 and D; thus, consulting with a dietitian is recommended. Additionally, it states that when cow’s milk is contraindicated, hypoallergenic formula is preferable.

Nutrition Considerations with Elimination Diets

Before beginning an elimination diet, it is essential for a dietitian to review the current diet. This helps assess potential risks of nutritional inadequacy, especially as the number of restricted foods increases. The dietitian will evaluate nutrition status, overall feeding behaviors and risks of deficiencies in essential nutrients like protein, calcium, and iron. As the diet changes, monitoring by a healthcare provider is important to prevent long-term issues, including the risk of feeding difficulties or texture aversions.

My Experience: Identifying and Filling Nutrient Gaps

After analyzing Cole’s diet on a 4-FED, I became aware that his intake of calories, fat, and essential vitamins like B-vitamins, calcium, and iron was insufficient. This was especially concerning as these nutrients are crucial for growth and development. Using supplemental AAF became an important strategy to fill these gaps. AAF provides a hypoallergenic nutrition source and has been shown to support children with food allergies and EoE by preventing nutritional deficiencies.

Final Thoughts

Managing EoE and elimination diets is challenging, both emotionally and nutritionally. Parents of children with EoE must balance restrictive diets with the nutritional needs of growing kids. From my experience with Cole, careful planning and regular monitoring are essential. Specialized nutritional supplements, like AAF, are often needed to ensure that nutritional gaps are filled.

The journey is not easy, but with support from healthcare professionals and dietitians, families can successfully manage EoE. With persistence and the right resources, families can successfully navigate the complexities of EoE and elimination diets.

Kelli Miller, MS, RD, LD has a Bachelor of Science degree in Food and Nutrition from Florida State University and Masters of Science in Health and Nutrition from the University of North Florida. She is a Registered Dietitian (RD) and a Board Certified Nutrition Support Clinician from 2012-2022. For more than twelve years, Kelli has worked in the clinical setting as an RD. She has specialized in pediatric nutrition for 9 of those years, specifically GI/Allergy, Critical Care, and Oncology. During her 6 years as a GI dietitian, she grew the nutrition clinics for Feeding Difficulties, IBD, Carbohydrate Malabsorption, Liver Transplant, Eosinophilic Gastrointestinal Disorders, and General GI. Kelli is currently employed by Ajinomoto Cambrooke as a Clinical Specialist focusing on gastrointestinal and allergy nutrition. She is also mom to a 7-year-old boy with Eosinophilic Esophagitis and strives to find ways to improve outcomes in children with GI and allergic medical conditions.