Background: Bone morphogenetic protein-4 (BMP-4) plays an important role during the embryonic development of tooth and bone. Studies have shown around 20% to 35% of Taiwanese exhibit an extra distolingual root, radix entomolaris, in the first mandibular molar. However, the association of the polymorphisms with the mandibular first molar exhibiting a distolingual root has never been evaluated. Methods: Two hundred Taiwanese were grouped using two different characteristics: subjects with and without distolingual roots. BMP-4 polymorphism was evaluated by polymerase chain reaction-restriction fragment length polymorphism, and compared among the groups for each characteristic. Results: Twenty four subjects showed the presence and 92 the absence of the root. The distributions of age, gender, and the habits of smoking, betel nut chewing, and drinking were similar in these two groups. No differences in genotype and allele distributions between the two subject groups were shown. This was regardless of the homo- and hetero-zygosity of C/ T, between TT and CT+CC, and between the alleles of T and C. Comparing the distribution of T or TT in the two subject groups, the odds ratio and the adjusted odds ratio in the genotypes and the allele of C were further confirmed with non-difference. Conclusions: The BMP-4 polymorphism may not be correlated with the presence of distolingual roots.