The system y(+) cationic amino acid transporters (CATs) play an important role in the regulation of lysine and arginine utilization. We have characterized the genomic organization and tissue transcription of the chicken CAT-2 (cCAT-2) isoforms from pectoralis muscle. The primary cCAT-2 transcript is alternatively spliced within the same position of the mRNA to produce cCAT-2A and cCAT-2B isoforms that share high nucleotide homology with their mammalian counterparts. We also identified a novel third CAT-2 isoform, cCAT-2C. This isoform contains a premature termination codon and studies in the chicken LMH cell line show that cCAT-2C mRNA is degraded by the nonsense-mediated mRNA decay pathway. All three cCAT-2 isoforms are transcribed in liver, pectoralis, gastrocnemius and heart. Chicken cCAT-2A was the predominant cCAT-2 isoform in liver, pectoralis and gastrocnemius. Analysis of the 5'-untranslated region of cCAT-2 identified multiple cCAT-2 promoters. Chicken CAT-2 promoter usage was tissue dependent and was not responsible for cCAT-2 isoform production. Analysis of genomic sequence upstream cCAT-2 promoter regions revealed binding sites for transcription factors involved in amino acid sensing, hormone signaling and immune function. These results provide insight into the role of the cCAT-2 gene and its regulation of lysine and arginine utilization in aves.