We report a case of a 4-week-old female neonate with Jeune's asphyxiating thoracic dystrophy (JATD) and coexistent situs anomaly, primarily presenting as gastric motility disorder. The child presented with abdominal distension and nonbilious vomiting since birth with failure to thrive. However, skeletal survey revealed JATD. Upper gastrointestinal contrast study showed situs inversus with delayed gastric emptying. Pyloric biopsy and intraoperative antro-duodenal manometry confirmed association of gastric motility disorder. Awareness of the unusual possibility of primary presentation of Jeune syndrome as gastric motility disorder will improve the management approach in such infants.