Our purpose was to describe the natural history of isolated neonatal swallowing dysfunction (INSD). Nine infants with INSD are described. Eight presented within two weeks of birth. Symptoms included choking and cyanotic spells with feeds, recurrent aspiration, apnea, stridor, and vomiting. Three had nonspecific neurological abnormalities and were diagnosed later in life with underlying disorders (myotonic dystrophy, CHARGE association, velocardiofacial syndrome). All required tube feeding. Six tolerated nasogastric feedings and received a gastrostomy tube. Three failed nasogastric feeds and required jejunal feedings. The gastrostomy tube was removed in 7/9 at a mean age of 37 +/- 9 months. In conclusion, INSD has a good long-term prognosis. The presence of minor neurological abnormalities at presentation suggests another underlying disorder. Nasogastric feeding followed by a gastrostomy is recommended in those without gastroesophageal reflux. Jejunal feedings are necessary in some. While most improve over time, they may need nutritional support for 3 years or more.