There is evidence of a relationship between tooth size and tooth agenesis in human populations, with a tendency for reduced tooth size in individuals with missing teeth. The aim of this study was to analyze the size of remaining teeth (mesiodistal crown diameters) and their variability in individuals with varying degrees of severity of congenitally missing teeth. Tooth crown diameters were recorded from 100 dental plaster casts of Japanese males. Subjects were divided into three agenesis groups: group A had one missing tooth per individual, group B had two missing teeth per individual, and group C had three or more missing teeth per individual. For comparison, tooth size data were used from a previously studied sample of Japanese males who did not have any congenitally missing teeth. Group A displayed the largest mesiodistal crown size dimensions for all maxillary and mandibular teeth, followed by group B, and then group C. In comparison with the reference data, when only one or two teeth were missing, the remaining teeth tended to be larger, but when there were three or more missing teeth, the remaining teeth tended to be significantly smaller throughout the dentition. In terms of tooth size variability, dental dimensions in the agenesis groups were generally more variable compared with those in the reference sample. This tendency was most pronounced in the group with the greatest number of missing teeth. Although there was a tendency for the size of the remaining teeth to be more reduced as the number of missing teeth increased, tooth size in individuals with only one or two teeth missing was generally larger than in a control group with all 32 permanent teeth, suggesting that the relationship between tooth size and dental agenesis may be more complicated than previously thought, perhaps due to local compensatory interactions affecting the size of teeth.