Four different transcripts of the Mecp2 gene can be distinguished by the length of the 3' untranslated region generated by usage of alternative polyadenylation sites. In situ hybridization analyses encompassing embryonic to 20-week postnatal age showed that transcripts are expressed in the central nervous system, with a progressive restriction during development culminating in localized strong expression in the cerebral cortex, olfactory bulb, hippocampal formation, and internal granule and Purkinje layer of the cerebellum. Real-time RT-PCR measurements of Mecp2 transcript levels showed variations with mouse age in two distinctive patterns that are unique to the central nervous system and the visceral organs, respectively. The 10-kb mRNA is the predominant form expressed in the brain in contrast to the shorter species expressed in the lung and liver. The developmental profile of Mecp2 mRNA highlights a potential tissue-specific function of the 3'UTR in the regulation of MeCP2 protein synthesis in response to the age-specific requirement of MeCP2 function during the life of the mouse.