Abstract The genetics of tooth root length have not been extensively studied. This study was conducted to identify the quantitative trait loci (QTLs) involved in the determination of root length in mice. Mesial, palatal and distal root length (MR, PR, and DR, respectively) of the upper first molar (M1) and DR of the lower first molar (M1) were measured in SMXA recombinant inbred (RI) strains of mice. For each trait, mean values of substrains of SMXA RI mice showed a continuous spectrum of distribution. A genome-wide linkage test detected QTLs exceeding the suggestive threshold levels for MR of M1 (chromosomes 1 and 9), PR of M1 (chromosomes 1, 11 and 19), DR of M1 (chromosomes 4, 11 and 19) and DR of M1 (chromosome 11 and 13). These findings suggest that a polygenic system is operative in the determination of tooth root length, and there is some independence of genetic determination among different roots.