Methyl-CpG binding protein 2 (MeCP2) is an epigenetic regulator in brain that binds to both methylated and hyroxymethylated DNA with similar affinities. MeCP2 has two isoforms, MeCP2E1 and MeCP2E2 with distinct N-terminus. These isoforms are generated by alternative splicing of the MECP2/Mecp2 gene. Despite the wealth of knowledge about the molecular properties of MeCP2 as a whole protein, little is known regarding its isoform components. Importantly, basic fundamental questions such as MeCP2 isoform-specific expression profile and the underlying regulatory mechanisms are yet to be fully addressed. To further explore the role(s) of MeCP2 isoforms, we have characterized MeCP2 isoform-specific expression profiles. In this study, we show that MeCP2 isoforms are differentially distributed in the adult murine brain, and are temporally expressed during mouse brain development. Our study allows us to gain further insight into the function(s) of MeCP2 isoforms in the central nervous system.