Taenia pisiformis (Cestoidea; Cyclophyllidea; Taeniidae) tapeworms infect the small intestine of canids and felines, such as dogs and foxes. Synonymous codon usage in T. pisiformis was examined through 8118 reconstructed annotations of transcriptome sequences. The mean value of GC content for the reconstructed genes was 49.48%. Twenty-four codons were determined as "optimal codons". Approximately all translational optimal codons (except CGU) ended on G or C. The gene positions on the primary axis were strongly positively correlated with GC content at the third codon positions and GC content of individual genes. At the same time, the gene expression level assessed by the CAI, the hydrophobicity and aromaticity of encoded proteins were correlated with the GC content at the third codon positions and the effective number of codons (ENC), respectively. We infer that the gene expression level, the hydrophobicity and the aromaticity of the encoded proteins also influenced codon usage in T. pisiformis. Knowledge of the codon usage pattern in T. pisiformis can improve our understanding of the mechanisms of biased usage of synonymous codons and can help in selecting appropriate host expression systems for potential vaccine genes of T. pisiformis. (C) 2012 Elsevier Inc. All rights reserved.