sponse in the rice seedling stage in a recombinant inbred (RI) population derived from a cross of a japonica variety, Asominori (lower GA3 response), with an indica variety, IR24 (higher GA3 response), using 289 RFLP markers. Continuous phenotypic variation of GA3 response index and transgressive segregation in both parental directions were observed, suggesting that GA3 response in regard to seedling plant height was a quantitatively inherited trait in the RI population. Five QTLs controlling GA3 response were identified and mapped to chromosomes 1, 3, 4, 6 and 12, respectively. Among them, the largest effect QTL (qGAR-1), located between G2200 and C86 on chromosome 1, explained 28.2–34.1% of the total phenotypic variation. The second largest effect QTL (qGAR-12) was detected near C751 on chromosome 12 and accounted for 13.2–16.5% of total variation. The remaining three QTLs on chromosome 3, 4 and 6, explained 5.1–6.4% of total phenotypic variation, respectively. In addition, alleles with increasing and decreasing GA3 response effects were detected from both parents. The molecular markers tightly linked to GA3 response QTLs lead to the isolation of loci and will help us to better understand GA3 response mechanisms in rice.