We report the case of a 17-year-old male with Seckel syndrome and horseshoe kidneys which had a 7 mm kidney stone in the lower pole calyx of the right moiety. The patient had a history of rotoscoliosis with 60° dextroconvex curvature and hepatic steatosis. Attempted ureteroscopy was unsuccessful due to stone location and anatomy. Percutaneous nephrolithotomy was ultimately required. This case highlights the difficulties of endoscopic treatments of renal calculi in patients with abnormal renal anatomy and dysmorphia. To our knowledge, this is the first reported case of nephrolithiasis in a patient with Seckel syndrome and horseshoe kidneys.