Immunoglobulin A (IgA) nephropathy (IgAN) is now considered the most common form of primary glomerulonephritis worldwide. It is characterized by predominantly mesangial IgA and C3 deposition, which is related to mesangial proliferative changes. Mesangial IgA deposition is incidentally encountered in asymptomatic individuals, but its precise frequency and significance had not been clarified. We performed zero-hour allograft biopsies in 510 renal transplantations (446 living donors, and 64 cadaveric donors) at the Kidney Center of Tokyo Women's Medical University. Mesangial IgA and C3 deposition were analyzed immunohistochemically, and the frequency and pathological features of mesangial IgA deposition were investigated. Mesangial IgA deposition was present in 82 (16.1%) of the total 510 allografts with no statistical difference between living donors (72/446, 16.1%) and cadaveric donors (10/64, 15.6%) or between blood-related donors (66/392, 16.8%) and nonblood-related donors (16/110, 14.5%). Histologic investigation of IgA(+) allografts revealed the frequency of mesangioproliferative glomerulonephritis was significantly higher in IgA(+)/C3(+) allografts (8/16, 50%) than in IgA(+)/C3(-) allografts (11/66, 16.7%). Moreover, the number of infiltrated macrophages to glomerulus (cells/glomerular cross section) was significantly higher in the IgA(+)/C3(+) allografts than in IgA(+)/C3(-), IgA(-)/C3(+) and IgA(-)/C3(-) allografts. The latent mesangial IgA deposition was a relatively common phenomenon in the healthy Japanese donors. This phenomenon was associated with mesangial proliferation and glomerular macrophage infiltration in some of the affected individuals, especially with combined IgA and C3 deposition. The results should provide insights into the epidemiology and pathogenesis of IgAN, the most common form of glomerulonephritis in many countries.