The polymorphisms of arylalkylamine-N-acetyltransferase (AA-NAT) gene in high-prolificacy Jining Grey goat, medium-prolificacy Boer goat and low-prolificacy Liaoning Cashmere, Inner Mongolia Cashmere and Angora goats were detected to analyse their relationships with litter size.Primers (P1-P5) were designed to detect the polymorphisms by PCR-SSCP and PCR-RFLP. For P2,AA, AB and BB genotypes were detected. Sequencing revealed one silent mutation (T132C) of AANAT gene in BB in comparison to AA. For P3, CC and CD genotypes were detected and sequencing revealed one mutation (C265T) of AA-NAT gene in CD in comparison to CC, and this mutation resulted in an amino acid change of Arg→Cys (R89C). The Jining Grey does with genotype CD delivered by 0.56 kids (P<0.05) more than those with CC genotype. For P5, EE, EF and FF genotypes were detected and sequencing revealed one mutation (C586T) of AA-NAT gene in FF in comparison to EE. This mutation caused an amino acid change of Arg→Trp (R196W). For both P2 and P5, the differences in litter size among three genotypes were not significant in Jining Grey goats (P>0.05).These results preliminarily indicate that allele D at the C265T locus of AA-NAT gene is a potential marker in genetic improvement of litter size in goats.