Transcranial sonography (TCS) has never been used in the evaluation of morphology of pineal gland. The aim of the study was to assess the possibility of TCS to distinguish normal from cystic pineal gland and to correlate its size with magnetic resonance imaging (MRI) at the first examination and during follow-up. Sixty patients with previously made MRI of the brain were evaluated by two independent observers using TCS, blinded to the results of the MRI. Inappropriate bone window limited TCS examination in seven patients. All 14 pineal gland cysts (PGC) seen on MRI were detected by both observers using TCS. Control group consisted of 39 healthy examinees. No statistically significant difference has been found between: PGC size measured by first and second observer by TCS (P = 0.425), PGC size measured by TCS and MRI (first observer, P = 0.353; second observer, P = 0.425), size of the pineal gland measured by TCS and MRI in control group (first observer, P = 0.497; second observer, P = 0.370) or interobserver variability in control group (P = 0.373). The MRI and TCS follow-up of ten patients after six months did not show any difference in size of PGC. TCS can be used as a method in detection, measurement and follow-up of PGC.