Body weight quantitative trait loci (QTLs), Bwq1 and Bwq2, identified previously in C57BL/6J x KK-Ay/a F2-Ay/a mice, were further confirmed and characterized. Body weight measurement was done from 21 days after birth (Day 21) through Day 100, at 10-day intervals. Bwq1 was statistically significant only on Days 40, 50, and 60, whereas Bwq2 was statistically significant on and after Day 40. When body weight gain (WG) between two successive weight measurements was evaluated, both Bwq1 and Bwq2 were statistically significant only for WG between Days 30 and 40. The results suggest that variations in body weight among F2-Ay/a individuals in later life have been determined by variations in WG during the period shortly after weaning. The results also suggest that Bwq1 is related to increased body weight in the KK strain, because the effect of Bwq1 on the body weight is observed not only in F2-Ay/a, but also in F2-a/a. On the other hand, it is suggested that Bwq2 is related to enhanced obesity caused by Ay mutation and therefore is a genetic modifier that specifically interacts with the Ay allele, because the effect of Bwq2 is only observed in F2-A y/a. There are two candidate genes, Pparg and Hrh1, which are located near the 95% confidence interval of Bwq2, and which are expressed in the adipose tissue; however, we could not find any nucleotide differences in both cDNAs between KK and C57BL/6J strains.