We present a male infant with hydrocephalus, cleft lip/palate, micrognathia, club foot, laryngeal stenosis and ostium secundum type atrial septal defect. The karyotype was 46 XY. The combination of malformations observed overlaps with the characteristic findings of hydrolethalus syndrome, Meckel syndrome, Smith-Lemli-Opitz syndrome and pseudotrisomy 13. We discussed the differential diagnosis of the case.