Many mammal species, including humans, exhibit oligodontia, or a lack of certain teeth in their dentition. However, the causes of the condition remain controversial. In the house musk shrew, Suncus murinus, both osteological and odontogenetic factors, which are genetically determined, have been implicated as causes of oligodontia. We examined 350 dry cranial specimens of S. murinus, representing seven laboratory strains and two wild populations. Oligodontia was observed in the upper third incisor (I(3)) and upper third premolar (P(3)); no supernumerary teeth were observed. None of the specimens with oligodontia had embedded teeth, as determined by soft X-ray. Congenital oligodontia was observed on P(3) and I(3). Moreover, the type and frequency of missing teeth differed among strains/populations. We compared the ratio of P(4)M(3) to PL as a possible cause of oligodontia. For P(3), we compared normal individuals to those with missing teeth within populations/laboratory strains, but did not detect significant differences. I(3) was compared among three laboratory strains: NAG (I(3) absent in 97%), TESS, and RYU (normal strains). TESS and RYU individuals had a longer distance from the upper fourth premolar to the upper third molar (P(4)M(3)), relative to palate length (PL), than NAG individuals. Specimens with oligodontia at I(3) and P(3) showed no difference in the ratio of P(4)M(3) length to PL. These findings suggest that osteological factors do not account for the absence of P(3) and I(3). Therefore, we believe that oligodontia in S. murinus depends on odontogenetic factors. In addition, as for I(3) and P(3)-absent, possibility related to some genes was thought about.