Cobalamin C (cbl C) deficiency, an inherited disorder of vitamin B12 metabolism, causes elevated levels of methylmalonic acid and homocysteine and decreased methionine in all body fluids. Renal complications of cbl C disease are thrombotic microangiopathy (TMA), chronic renal failure, tubulointerstitial nephritis and proximal renal tubular acidosis. There is, however, only one case report of primary glomerular pathology, focal segmental glomerulosclerosis, in a cbl C deficient patient. We report a case of an atypical glomerulopathy in a 16-year-old male patient with cbl C deficiency. The glomerulopathy manifested with proteinuria and progressive renal insufficiency. The renal histologic, immunofluorescent and ultrastructural findings were similar, but not identical, to idiopathic membranoproliferative glomerulonephritis (MPGN) but also overlapped with those of a TMA. The serum complement profile was normal; there were scanty glomerular deposits of C3, no deposits of IgG and ultrastructural findings that were similar to those seen in either MPGN type III or a TMA. On the basis of these findings we have designated the renal disease as an atypical glomerulopathy.