Objectives Cysteamine prevents organ damage in children with cystinosis, but may cause gastrointestinal (GI) symptoms.In this study we evaluated the nature of GI disease, and the value of omeprazole in controlling GI symptoms in these children.Study design Upper GI disease was evaluated with endoscopy, gastrin levels, and acid secretion studies after oral administration of cysteamine, before and after 16 weeks of therapy with omeprazole. A symptom score was devised.Results Eleven children (mean age, 5.7 years) were studied. After cysteamine ingestion, before and after omeprazole therapy, the mean maximum acid output was significantly higher than the mean basal acid output. The maximum acid output was measured within 60 minutes of cysteamine ingestion and was reduced by omeprazole therapy (P < .01). The mean peak gastrin level was 30 minutes postcysteamine and was higher than baseline (P < .01). The initial mean symptom score (maximum score, 14) was 6.9 and fell to 0.7 (P < .0001) after 16 weeks of omeprazole therapy. At endoscopy, two children had diffuse gastric nodularity, and nearly all had cystine crystal deposits.Conclusions GI symptoms in children with cystinosis receiving cysteamine are often acid-mediated and improve with omeprazole. Cystine crystals were detected in the GI tract and may signify inadequate treatment with cysteamine. (J Pediatr 2003;143:224-30)