In general, tuberculosis (TB) is more common in men than women. However, for reasons currently not understood, women are 1·5–2 times more likely to report TB compared to men in Pashtun region (Afghanistan, adjacent provinces Pakistan and Iran). We explored whether or not gender disparity in TB notifications in the Pashtun region of Pakistan can be explained by Pashtun ethnicity. Using an ecological linear regression design, we estimated the effect of Pashtun ethnicity on female-to-male ratio (FMR) in TB notifications after adjusting for other determinants of women's health, in Pakistan. Districts with a high proportion of women of Pashtun ethnicity had a 44% (95% confidence interval 27–61) increase in FMR of notified TB cases compared to those with low proportions, after controlling for confounders. Genetic predisposition and distinct socio-cultural determinants could be possible causative factors. However, these hypotheses need further evaluation through rigorous longitudinal studies.