The present paper emphasizes on the histopathological effects of an azo dye, Direct Green 6 on the kidney and gills of Labeo rohita by light microscopy. Fingerlings were exposed to sublethal concentrations (2.5, 5.0 and 10.0 ppm) of dye for 5, 10 and 15 days to study histopathological changes. No histopathological changes were seen in the kidney and gills of control fingerlings. Unlike control fingerlings, both the target organs showed some histopathological changes. Fingerlings exposed to 2.5 ppm concentration of the dye showed shrinkage of glomerulus, increased peritubular space, decreased lumen while 5.0 ppm produced haemorrhage in the interstitial tissue and mild degeneration in the kidney. Necrosis in the tubular epithelium, distruction of cell membrane and loss of cellular cytoplasm were observed in kidney of fingerlings exposed to 10 ppm dye concentration. Gills of fingerlings exposed to 2.5 ppm of dye showed aneurism and mild degenerated central axis. 5 ppm of dye concentration produced remarkable changes like epithelial lifting, hyperplasia, enlarged and vacuolated cartilage cells. Haemorrhagic tip, fusion and curling of secondary gill lamellae and at some places complete removal of them were also observed in gills of fingerlings exposed to 10 ppm.