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Although genes on the human X chromosome reportedly influence tooth crown morphology, little is known about X chromosome activation or inactivation systems relevant to morphological variations. We assessed the relationships between tooth crown size and crown morphological traits in females with Turner syndrome, the variants of which include complete absence of one X chromosome, lack of the short arm (Xp), or duplication of the long arms (Xq), and then estimated the functions of Xp and Xq in the process of unilateral X chromosome inactivation during tooth crown development. The mesiodistal and buccolingual diameters in the maxillary first (M1) and second (M2) permanent molars were compared among X chromosome karyotypes by multiple regression analyses, and their relationships with the development of Carabelli's cusp and the distolingual cusp were analyzed using logistic regression analysis. The crown sizes increased in the order of the 46,X,i(Xq) karyotype, 45,X and 45,X/46,XX karyotypes, and control group. A lower frequency of Carabelli's cusp and higher frequency of a reduced distolingual cusp in M1 were characteristics of Turner syndrome. The overall M1 and M2 crown sizes differed among the X chromosome karyotypes, whereas a smaller crown size was associated with a reduced distolingual cusp but not with Carabelli's cusp. Considering the differences in chromosome arrangement among females with Turner syndrome and the process of unilateral X chromosome inactivation, the observed results can be considered in terms of quantity or number of promoters/inhibitors during tooth crown development. The X chromosome karyotypes have a strong influence on the overall crown sizes of the M1 and M2 molars because those karyotypes with variable numbers of active gene regions directly influence tooth germ development in an early stage of human odontogenesis. The later forming cusps, such as the distolingual cusp and Carabelli's cusp, may be affected by this developmental prerequisite.