Background: Microscopic hematuria without proteinuria is a common clinical finding in cases of immunoglobulin A (IgA) nephropathy and of thin basement membrane nephropathy. Liver-type fatty acid-binding protein (L-FABP) is expressed in renal proximal tubules and is reported to be a useful marker of the progression of chronic glomerulonephritis. Aim: To assess urinary L-FABP levels for differential diagnosis in patients with microscopic hematuria but without proteinuria. Methods: This was a multi-center retrospective study. Thirty adult patients who underwent renal biopsy for microscopic hematuria and 20 healthy adult volunteers were included in this study. Urinary L-FABP levels were measured by enzyme-linked immunosorbent assay and compared, particularly between those diagnosed with IgA nephropathy and those diagnosed with thin basement membrane nephropathy. Results: Twelve (40%) patients had IgA nephropathy, 6 (20%) had thin basement membrane nephropathy and 12 (40%) had normal biopsy findings. The urinary L-FABP level was significantly higher in patients with IgA nephropathy (38.4 ± 26.8 µg/g Cr) than in healthy subjects (5.8 ± 4.0 µg/g Cr) (p < 0.01); however, the level in patients with thin basement membrane nephropathy or normal biopsy results was comparable to that in healthy subjects. Follow-up data were available for 11 of the 12 patients with IgA nephropathy who initially had no proteinuria. After 24 months, 4 of the 11 were found to have proteinuria, and the urinary L-FABP level had increased from 40.6 ± 30.5 µg/g Cr to 58.8 ± 40.5 µg/g Cr (p < 0.01). Conclusions: Our data suggest that the urinary L-FABP level can be used to discriminate between IgA nephropathy and thin basement membrane nephropathy in patients with microscopic hematuria.