Intraspecific variation in the number of vertebrae is common and taxonomically widespread, although the possible adaptive significance of this variability remains poorly understood. If body size is influenced by the number of vertebrae, then an increased number of vertebrae could facilitate reaching a large body size, and provide a proximate explanation for sex and population differences in mean body size. We tested these predictions using data from 12 populations of nine-spined sticklebacks (Pungitius pungitius), which are known to differ genetically in mean body size, as well as to show a high degree of female-biased sexual size dimorphism. After controlling for the confounding effects of habitat, sex, and population of origin, there was weak and habitat-specific positive association between body size and the number of vertebrae. However, viewed across different populations, there was no correlation between mean body size and the number of vertebrae. Similarly, although females (the larger sex) had, on average, more vertebrae than males, the degree of sexual dimorphism in the number of vertebrae and body size were uncorrelated across populations. Furthermore, there was no relationship between latitude and the mean number of vertebrae, revealing that vertebral numbers in the nine-spined stickleback do not follow Jordan's rule (i.e. increase with increasing latitude). Taken together, the results obtained in the present study suggest that vertebral number only has a very limited influence on intraspecific patterns of body size variation in the nine-spined stickleback.