Weight gain and body fat increase the risk of cardiometabolic disease. Cross-sex hormone therapy in transgender persons leads to changes in body weight and body composition, but it is unclear to what extent. We performed a meta-analysis to investigate the changes in body weight, body fat and lean body mass during cross-sex hormone therapy in transgender persons. We searched the PubMed database for eligible studies until November 2015. Ten studies reporting changes in body weight, body fat or lean mass in hormone naive transgender persons were included, examining 171 male-to-female and 354 female-to-male transgender people. Pooled effect estimates in the male-to-female group were +1.8 kg (95% CI: 0.2;3.4) for body weight, +3.0 kg (2.0;3.9) for body fat and −2.4 kg (−2.8; −2.1) for lean body mass. In the female-to-male group, body weight changed with +1.7 kg (0.7;2.7), body fat with −2.6 kg (−3.9; −1.4) and lean body mass with +3.9 kg (3.2;4.5). Cross-sex hormone therapy increases body weight in both sexes. In the male-to-female group, a gain in body fat and a decline in lean body mass are observed, while the opposite effects are seen in the female-to-male group. Possibly, these changes increase the risk of cardiometabolic disease in the male-to-female group.