AIMS--To investigate the morphological and histopathological associations between an individual pit seen on stereomicroscopy or magnifying colonoscopy and an individual crypt seen in histological sections; and to examine these associations in colorectal tumours. METHODS--Fourteen thousand and twenty three cases were examined by colonoscope at Akita Red Cross Hospital. The surface mucosal pits of the lesions were observed using a magnifying endoscope in vivo and the pits of the extracted specimens were observed in vitro using a stereo microscope. Histological diagnoses were determined by light microscopy: the pit patterns in 100 glands were analysed. RESULTS--Pit pattern was classified into seven principal types: (1) normal round pit; (2) small round pit; (3) small asteroid pit; (4) large asteroid pit; (5) oval pit; (6) gyrus-like pit; and (7) non-pit. There was a correlation between pit pattern and the structure of the underlying crypt or gland. Furthermore, there was an association between pit pattern and the histology of the cells in the gland. Macroscopically, types 3, 4, 5, and 6 were common in protruding lesions. Type 2 was common in depressed lesions. The non-pit pattern was recognised in both. The depressed lesions had invaded the deeper layers more rapidly than protruding lesions. CONCLUSIONS--There were associations between individual pits and crypts. The branching carcinoma gland is thought to be the result of malignant transformation of the adenoma gland. The straight carcinoma gland is thought to result from the normal gland becoming malignant. The gland of the small round pit is thought to change from normal to the straight carcinoma gland via malignant transformation.