Intestinal malrotation is a relatively uncommon condition with diverse outcomes. Familiarity with variations in the presentation of malrotation is imperative as early diagnosis and prompt subsequent surgical intervention are essential to optimizing outcome. The most frequent clinical sign in the neonate is bile-stained emesis. We report three cases of unsuspected malrotation that were diagnosed in neonates with a history of nonbilious emesis who were assessed for presumed gastroesophageal reflux or aspiration. Gastroesophageal reflux is a common condition among newborns, and can be a subtle presentation of malrotation. Clinicians should consider malrotation as a possible cause of reflux, particularly in infants with unusually pathologic or persistent symptoms necessitating ongoing treatment for reflux.