The aim of the present study was to evaluate the value of identifying fluid-fluid level via preoperative magnetic resonance (MR) images in differentiating pituitary adenomas from craniopharyngioma, Rathke's cleft cyst (RCC), and other cystic sellar-suprasellar lesions. The data of 293 consecutive patients who underwent surgery for sellar-suprasellar lesions between July 2010 and December 2012 was retrospectively reviewed, and a total of 133 cystic cases were included in the present study. MR images and pathological features of all subjects were examined. Among the 133 cystic sellar-suprasellar masses, there were 78 cases of pituitary adenomas, 31 cases of craniopharyngioma, 21 cases of RCC, one case of epidermoid cyst and two cases of abscess. Fluid-fluid levels were identified n 43 cases (55.13%) of cystic pituitary adenomas, with a single fluid level in 23 cases, two fluid levels in 8 cases, and three levels or more in 12 cases. Two cases (6.45%) of craniopharyngioma, and one case (4.76%) of RCC presented single fluid level. No instances of fluid-fluid levels were observed in epidermoid cyst or abscess. Fluid-fluid levels were typically exhibited on axial T2-weighted images. The identification of fluid-fluid level in cysts provides useful diagnostic value in distinguishing pituitary adenoma from other sellar-suprasellar lesions. The findings of the present study suggest that a sellar-suprasellar mass with a fluid-fluid level inside the tumor is most likely a pituitary adenoma, particularly if multiple fluid levels are observed in the same tumor. The fluid-fluid level is typically clearly depicted on axial or sagittal MR images, suggesting subacute or chronic hemorrhage in pituitary adenomas.