Drought is an important constraint to productivity in rainfed rice environments. Improvement in the various components of rice drought tolerance is now possible through the identification and manipulation of DNA markers linked with genes controlling these quantitative traits. A recombinant inbred line population was derived from the cross IAC165 x Co39. A molecular map was built that contained 182 RFLP and microsatellite markers. Segregation distortions were limited to a few chromosomal segments. Constitutive root traits, including maximum root length, root thickness and root dry weight in various layers, were measured on 125 lines in a greenhouse replicated experiment. QTL analysis was performed using composite interval mapping. Between 1 and 4 main effect QTLs, which explained individually between 5.5 and 24.8% of the variability, were identified for each trait. The most important genomic regions, which carried QTLs for several traits, were found on chromosomes 1, 4, 9, 11 and 12. The QTL locations were in good agreement with previous studies on these traits, confirming the value of the QTLs in a different genetic background. Epistasis represented a non-negligible component of the observed variability for some of the traits but was not detected for others. These results add to the understanding of the genetic control of root morphology in rice, which is necessary to strengthen marker-aided selection programs to improve varieties for water-limited environments.