Background Klippel-Trénaunay syndrome (KTS) is a rare congenital condition characterized by the clinical triad of capillary malformations (port wine stains), varicose veins with or without venous malformations, and bony and/or soft tissue hypertrophy. Case presentation Here we report the first case of a one-day-old male with KTS presenting with crossed-bilateral limb hypertrophy and post-axial polydactyly. Conclusion This case serves to highlight the variable presentation and multiple problems faced by patients with KTS and why multidisciplinary management is mandatory.