The application of MRI to 167 Holstein cows and 76 Japanese black cows made it possible to distinguish two types of residual cleft cysts (RCCs) in their pituitary glands on the basis of the differences in signal intensity: fluid-filled lesions with an intensity equal to that of cerebrospinal fluid (CSF) (hypointense on T1-weighted images and hyperintense on T2-weighted images); and solid lesions that were hypointense compared with cerebral parenchyma and isointense with CSF on T1-weighted images, and hypointense compared with cerebral parenchyma on T2-weighted images. Solid material was observed in lesions with a mean (sd) diameter of 2.09 (1.28) mm in 56 (33.5 per cent) of the Holstein cows, and in lesions with a mean diameter of 1.91 (0.89) mm in 20 (26.3 per cent) of the Japanese black cows. Four of the Holstein cows had RCCs more than 7 mm in diameter. Long-term development of the RCCs was suggested by histological findings of epithelial stratification and a structural shift from having a single to a stratified epithelial layer within the residual clefts of the affected pituitary glands.