Mutations in the gene for epsilon sarcoglycan (epsilon-SG) are associated with a disorder of the central nervous system, the myoclonus-dystonia syndrome (MDS; DYT11). In contrast, mutations of other sarcoglycan family members lead to limb-girdle muscular dystrophies. To establish the framework for functional studies of epsilon-SG, we cloned rat epsilon-SG cDNA, quantified epsilon-SG mRNA levels in neural and non-neural tissues at different developmental time points with relative quantitative multiplex real-time reverse transcriptase PCR (RT-PCR), and characterized the distribution of epsilon-SG mRNA in brain with in situ hybridization. Rat epsilon-SG cDNA contains an open reading frame (ORF) of 1311 bp that encodes a 437-amino acid (aa) protein with 95.9% and 98.2% identity to human and mouse epsilon-SG amino acid sequences, respectively. Using real-time RT-PCR, epsilon-SG was detected in both neural (cerebellar cortex, striatum, cerebral cortex, thalamus, hippocampus) and non-neural (muscle, liver, kidney, heart) tissues at each developmental time point tested [Embryonic Day 20 (E20), Postnatal Day 1 (P1), P7, P14, P36, 6 months, 1.5 years). Levels of epsilon-SG mRNA were highest at E20 in all tissues. The developmental regulation of epsilon-SG mRNA expression was most striking in muscle with E20 and early postnatal epsilon-SG mRNA levels over 10 times higher than those seen in adult rats. In adult rats, epsilon-SG mRNA levels were several-fold higher in brain, particularly cerebellar cortex, than in muscle. Radioactive in situ hybridization showed that epsilon-SG mRNA was widely distributed in rat brain. Robust hybridization signal was obtained from regions with dense neuronal packing such as the hippocampus, cerebellar molecular layer, and cerebral cortex. Our results suggest that epsilon-SG participates in the development of both neural and non-neural tissues and contributes to neuronal structure in the adult central nervous system.