Epithelial protein lost in neoplasm (EPLIN) is a cytoskeleton-associated protein that is down-regulated in transformed cells. Two EPLIN isoforms (alpha and beta) are generated by alternative promoter usage from a single gene. In pigs EPLIN was preferentially expressed in the muscle of splay-legged piglets, but not in the healthy ones, suggesting that it plays an important role in muscle development. A precise mRNA expression analysis through muscle development could shed some light on the EPLIN function associated with splayed legs. This article describes the isolation of the two alternative splice variants of EPLIN mRNA in pigs. The chromosome assignment and several polymorphism sites were also identified to lay a foundation for potential breeding applications. Gene expression analysis by real-time polymerase chain reaction (PCR) showed that both of transcripts were expressed in almost all tissues examined but in variable amounts in adult pigs. The temporal expression analysis indicated that they are not coexpressional through muscle development: EPLIN-alpha was detected in developing skeletal muscle, but EPLIN-beta was not.