The chromosomal region 15q11-q13 contains 47 copies of a brain-specific small nucleolar RNA (snoRNA), HBII-52. Kishore et al. now show that this snoRNA regulates alternative splicing of a specific pre-messenger RNA encoding a serotonin receptor by masking an exonic silencer. This snoRNA is not expressed in patients suffering from Prader-Willi syndrome and causes patients to express different isoforms of this serotonin receptor. Previously, it has been unclear how the loss of the Prader-Willi-imprinted region causes the disease, because most of its genes do not encode protein.