In this study, we attempted to use amplified fragment length polymorphism (AFLP) in combination with selective genotyping to detect loci that affected shank length and body weight at 10 weeks of age in Japanese quail (Coturnix japonica). A total of 88 primer pairs were used in AFLP analyses of 10 and 13 males with the longest and shortest shank lengths, respectively, from an F₂ intercross population derived from lines differentiated by large and small body size (LL and SS, respectively). Ten AFLP bands differed strikingly in frequency between the two groups (P<0.005). Genotyping of the 10 bands in 10 females with the longest shank lengths and 10 with the shortest revealed that one band differed significantly in frequency between the two groups for both males and females (P<0.05). This fragment shared 86.4% identity with a 361-bp sequence of chicken chromosome 1 located from position 51,672,791 to 51,673,152, as determined by chicken BLAT search. Polymerase chain reaction and sequence analysis revealed that a 190-bp insertion/deletion was the causal polymorphism. Genotypes of this indel marker were associated significantly with shank length and body weight in the F₂ intercross population (P<0.005). The insertion allele had a positive effect on both traits. To confirm the association of this marker with the two traits, we conducted association analysis in a population derived from heterozygous quails of another line. In this analysis, the indel genotypes showed no significant association with shank length or male body weight (P>0.05), but did show a significant association with female body weight (P<0.05).