OBJECTIVE: To describe the prevalence and characteristics of pineal cysts found on MRI in children. METHODS: This is a retrospective monocentric study of all brain magnetic resonance imaging (MRI) examinations performed under the same technical conditions for checking the idiopathic nature of short stature (ISS group, n = 116) and for the investigation of central precocious puberty (CPP) over a 3-year period (n = 56). Dimensions, wall and septal thickness, number of locules, signal intensity, and the presence of a solid component were analysed. Ten of 19 cysts were re-evaluated (follow-up interval 4-28 months). The prevalence of the pineal cysts was compared between the two groups using χ2 and Fisher's exact tests, and a significance threshold of p < 0.05. RESULTS: The prevalence of cysts was comparable in the two groups, CPP (10.7%) and ISS (11.2%). Cyst characteristics were similar in the two groups and 74% had thin septations. None of the cysts changed on follow-up. None of the children with pineal cysts exhibited neurological signs. CONCLUSION: Benign pineal cysts are a common finding in young children. High-resolution MRI demonstrates that these cysts are often septated. This pattern is a normal variant and does not require follow-up MR imaging or IV contrast media.