Cathepsin D (CTSD), a major ubiquitously expressed aspartic protease, is not only involved in muscle protein degradation, but also related to some pathological processes. In this study, we characterized the full-length cDNA, genomic DNA sequence, expression profile and polymorphism of the porcine CTSD gene. The full-length cDNA of porcine CTSD gene and the predicted protein sequence shared high identities wih other mammalian orthologous. Northern-blot analysis and Reverse transcription (RT)-PCR results indicated that the CTSD gene has one transcript of approximately 2.0 kb in normal tissues and was expressed ubiquitously in pigs, without significant differences in porcine heart, liver, spleen, lung, kidney, stomach, fat, triceps brachi, biceps femoris, and longissimus muscles. The porcine CTSD gene spans approximately 9.0 kb including nine exons. All exon/intron boundaries adhere to the GT/AG rule. Altogether 35 nucleotide polymorphisms of CTSD gene were discovered between Duroc, Landrace, Erhualian, and Dahuabai pigs. These polymorphisms included three missense mutations, eight synonymous mutations, and 24 intronic substitutions, and most polymorphisms are located in the intron 4 and 5. Three polymorphisms were genotyped in Duroc, Landrace, Dahuabai, and Erhualian pigs by PCR-RFLP method, and significant differences of their genotype frequencies were observed between Chinese native breeds (Dahuabai and Erhualian) and western breeds (Duroc and Landrace).