Seven single nucleotide polymorphisms (SNPs) were identified by PCR-SSCP and sequencing in the chicken apoA5 gene in F2 chickens from an experimental cross of White Plymouth Rock × Silkies. One SNP(C-169T) located on the 5′-regulatory region, another two in the second exon were transitions of C to T (600) and T to C (635). Four SNPs in the third exon were found, which were C841G, C914T, C1142G, C1394T. The association of the polymorphisms with carcass traits was investigated. The most significant results were yielded from primer apoA3F/R: the abdominal fat weight of CC chickens were significantly higher than that of AA, AB, AC, BB and BC chickens (P<0.05); AC chickens had lower liver weight than that of AA, AB, BB, BC and CC (P<0.05); BC chickens had lower heart weight than that of BB (P<0.05).