Some small nucleolar RNAs (snoRNAs) are exclusively expressed in the brain but they have no known role in higher brain function. We analysed the expression pattern of four brain-specific snoRNAs: MBI-36, MBII-48, MBII-52 and MBII-85, in mouse brain using in situ hybridization. All of these genes were expressed in the hippocampus and, except for MBII-85, their levels in ventral parts were higher than those in dorsal parts. Using quantitative real-time polymer chain reaction we determined hippocampal expression changes after contextual fear conditioning in mice. Ninety minutes, but not 25 h, after conditioning, we observed significant downregulation of MBII-48 and upregulation of MBII-52. Our finding that the expression of MBII-48 and MBII-52 is regulated during learning suggests that these snoRNAs have an important role in higher brain function.