Objective：To analyze the relationship between position of Rathke’s cleft cyst and pituitary gland by MRI and to explore its differential diagnostic value. Methods：Totally 48 cases of Rathke’s cleft cyst proved by the operation and pathology were served as cyst group，while 18 cases of pituitary adenoma which were misdiagnosed as Rathke’s cleft cyst were served as control group. The relationship between position of Rathke’s cleft cyst and pituitary gland in the coronal and sagittal plane was analyzed with MRI and was detected for statistical analysis. Results：（1）In the coronal plane，lesions locating in the middle of pituitary occurred more often in cyst group than in control group with statistical differences（corrected ?字2=37.898，P=0.000）. （2）In the sagittal plane，there were three kinds of position relationship between the cyst and the anterior and posterior lobe of the pituitary gland in cyst group. The kind that the cysts were located between the anterior and posterior lobe of the pituitary gland was the most common（38 cases，79.2%）. While in control group，14 cases of pituitary adenoma were located in the anterior lobe，except for 4 cases whose position relationship with the anterior and posterior lobe of the pituitary gland was indistinguishable. （3）In the sagittal plane，all lesions and pituitary stalk appeared at the same level in cyst group. The upper edge of the cysts was usually located behind the connection of pituitary stalk and pituitary（32 cases，66.7%）. While in control group，the pituitary adenoma and pituitary stalk appeared at the same or different levels and 12 cases（66.7%） appeared at the same level of pituitary stalk. It is rare that the upper edge of the pituitary adenoma was located behind the connection of pituitary stalk and pituitary（1 case，8.3%）. Statistical analysis showed significant differences in the occurrence rate of the lesions whose upper edge was located behind the connection of pituitary stalk and pituitary（corrected ?字2 test，?字2=10.947，P=0.001）. Conclusions：Relationship between position of Rathke’s cleft cyst and pituitary gland has some rules to follow and there is a big difference between with Rathke’s cleft cyst and pituitary adenoma. It has higher value in diagnosing Rathke’s cleft cyst when the cyst is located in the middle of pituitary in the coronal plane and seated between the anterior and posterior lobe of the pituitary gland with its upper edge situated behind the connection of pituitary stalk and pituitary in the sagittal plane.