Children with neurodevelopmental disabilities such as cerebral palsy (CP), spina bifida, or inborn errors of metabolism frequently have associated gastrointestinal problems. These include oral motor dysfunction leading to feeding difficulties, risk of aspiration, prolonged feeding times, and malnutrition with its attendant physical compromise. Gastrostomy tube feeding is increasingly being used in these children to circumvent oral motor dysfunction and prevent malnutrition. Foregut dysmotility causes several problems such as dysphagia from oesophageal dysmotility, gastro-oesophageal reflux disease, and delayed gastric emptying. Gastro-oesophageal reflux disease is common in these children but often fails to respond to medical management and may require surgical treatment. Finally, constipation is often a problem that may be overlooked in this population. This article focuses on these associated gastrointestinal manifestations and discusses the current diagnostic and therapeutic options available.