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Background An increasing number of families with children who have spinal muscular atrophy (SMA) are incorporating a special amino acid diet into their child's feeding regimens. Characteristics of the diet include high‐carbohydrate and low‐fat content with added probiotics. However, because of insufficient evidenced‐based research, clinicians are unable to prescribe or endorse this diet. Our aim was to assess the tolerability of an adapted version of the traditional amino acid diet in children with SMA type I. Methods Children with SMA type I were recruited if they were enterally fed and experienced at least one gastrointestinal symptom (reflux, vomiting, constipation, and/or diarrhea). Children were transitioned to an amino acid formula (Neocate Syneo‐Nutricia) for 8 weeks. Feeding tolerance was measured weekly by telephone consultation to monitor reflux, vomiting, stool consistency, and frequency. Results Fourteen children were recruited, the mean age was 4.1 years (±1.2 SD), and 64% of participants were female. The mean resting energy expenditure determined by indirect calorimetry was 51.5 kcal/kg (±7 SD). The most common gastrointestinal complaint before switching to the amino acid formula was constipation, which was reported in 12 of 14 (85%) patients, of which 10 of the 12 (83%) children required daily stool softeners/laxatives to help regulate bowel function. After 8 weeks on the amino acid formula, 10 out of 12 (83%) children stopped or reduced constipation medication. Conclusion Children with SMA type I who display gastrointestinal symptoms such as constipation and reflux may benefit from an amino acid formula that is fortified with probiotics.