The spectrum of pathology in native kidney biopsies varies considerably between different countries. Based on similar biopsy policy and joint workup, biopsy data of native kidneys of children in Yerevan (Armenia) and Zurich (Switzerland) were compared over a period of two decades (1993-2002 and 2003-2012). A total of 487 renal biopsies in Yerevan (EVN), n = 253; median age 11.2 years (range 0.8-18; 56 % males) and in Zurich (ZRH), n = 234; median age 8.7 years (range 0.1-18; 61 % males) were analyzed. Biopsies from EVN were locally analyzed by light microscopy (LM) and sent to ZRH for electron microscopy (EM) and immunohistochemistry. Biopsies from ZRH were evaluated by LM, EM, and immunofluorescence. The significant difference concerns the high frequency of amyloidosis in EVN (25.4 % in the first and 19.4 % in the second decade vs. 0 % in ZRH) and of IgA nephropathy in ZRH (30.2 % in the first and 26.1 % in the second decade vs. 8.1 in EVN). Certain forms of glomerulonephritis (membranoproliferative type I and membranous) and primary focal segmental glomerulosclerosis tended to be more frequent in EVN than in ZRH. Amyloid nephropathy due to familial Mediterranean fever is still highly frequent in Armenia with a slight decrease in the second decade. In Switzerland, the most common finding was IgA nephropathy.