We have isolated 14 differentially displayed and 10 further expressed sequence tags (ESTs) from Musculus biceps femoris of newborn healthy and splay leg piglets. By comparison with EMBL/GenBank data we could identify nine porcine homologues to human genes (TATA box binding protein associated factor B TAF1B; B-cell CLL/lymphoma 7B BCL7B; pyruvate dehydrogenase kinase, isoenzyme 4 PDK4; ribosomal protein S10 RPS10; SPARC-like 1 SPARCL1; epithelial protein lost in neoplasm beta EPLIN; N-myc downstream-regulated gene 2 NDRG2; pleiomorphic adenoma gene like 2 PLAGL and, BCL-2 associated transcription factor short form BTFS). Eight fragments correspond to uncharacterized ESTs and 7 ESTs had no significant match with database sequences. These data provide the first expression profiles in skeletal muscle of neonatal piglets and are a basis for candidate gene investigations for congenital splay leg in piglets. Eleven ESTs were physically mapped to porcine chromosomes 1, 3, 4, 5, 7, 8, 9 and 10 and contribute to the comparative map of humans and pigs.