Congenital liver cysts are an unusual finding and present a difficult diagnostic challenge. In a 5-month-old infant, routine echocardiography detected a cystic lesion (3 cm in diameter) just below the diaphragm. All conventional diagnostics, including magnetic resonance imaging (MRI), failed to clarify its etiology definitively. Moreover, a phrenic irregularity was suspected at the site of Morgagni. Finally, laparoscopy (5-mm scope and instruments) confirmed the diagnosis of a solitary liver cyst and a diaphragmatic defect. Using a Harmonic scalpel, the cyst was resected and the diaphragmatic defect was closed with interrupted nonabsorbable sutures. The patient's postoperative course was uneventful. Pathological analysis showed a true liver cyst with mesothelial lining and hepatic residues. Retrospective speculation suggests a common embryologic origin for both malformations. In conclusion, laparoscopy allowed final diagnosis and simultaneous treatment of an infant with the rare combination of a liver cyst and a diaphragmatic defect. To our knowledge, this case represents the first endosurgical experience of such a simultaneous procedure.