In this paper we present a three-dimensional (3D) morphometrical assessment of human tibia sexual dimorphism based on whole bone digital representation. To detect shape-size and shape differences between sexes, we used geometric morphometric tools and colour-coded surface deviation maps. The surface-based methodology enabled analysis of sexually dimorphic features throughout the shaft and articular ends of the tibia. The overall study dataset consisted of 183 3D models of adult tibiae from three Czech population subsets, dating to the early medieval (9-10th century) (N = 65), early 20th century (N = 61) and 21st-century (N = 57). The time gap between the chronologically most distant and contemporary datasets was more than 1200 years. The results showed that, in all three datasets, sexual dimorphism was pronounced. There were some sex-dimorphic characteristics common to all three samples, such as tuberosity protrusion, anteriorly bowed shaft and relatively larger articular ends in males. Diachronic comparisons also revealed substantial shape variation related to the most dimorphic area. Male/female distinctions showed a consistent temporal trend regarding the location of dimorphic areas (shifting distally with time), while the maximal deviation between male and female digitized surfaces fluctuated and reached the lowest level in the 21st-century sample. Sex determination on a whole-surface basis yielded the lowest return of correct sex assignment in the 20th-century group, which represented the lowest socioeconomic status. The temporal variation could be attributed to changes in living conditions, the decreasing lower limb loading/labour division in the last 12 centuries having the greatest effect. Overall, the results showed that a surface-based approach is successful for analysing complex long bone geometry.