Children growth and development may be affected by metal exposure. The objective of the present study was to investigate the interactive effects of age and gender on children hair toxic metal levels in urban environment of two Russian cities. A total of 2021 children living in Moscow and Novosibirsk aged 1–18 years old were examined. Hair Al, As, Cd, Hg, Ni, Pb and Sn levels were assessed using inductively-coupled plasma mass-spectrometry in dynamic reaction cell mode. Children from Novosibirsk were characterised by higher hair Al (37%), As (385%), Cd (127%), Hg (11%), Ni (23%), Pb (72%) and Sn (25%) in comparison to Moscow values. In the general cohort, boys had higher Al (13%), As (51%), Cd (65%), Pb (63%) and Sn (18%) levels, whereas hair Ni was higher in girls (17%). Further analysis demonstrated age-specific gender differences. In particular, only hair Ni and Cd levels were higher in male toddlers and pre-schoolers from Novosibirsk as compared to females. No gender difference was detected in Moscow. Maximal gender differences in hair metal levels were detected in adolescents for both locations. International Union of Pure and Applied Chemistry (IUPAC) reference values for all groups were also calculated. The overall reference limits for the studied children population were Al (1.335–3.340 µg/g), As (0.021–0.384 µg/g), Cd (0.000–1.389 µg/g), Hg (0.024–0.722 µg/g), Ni (0.076–0.701 µg/g), Pb (0.050–1.490 µg/g) and Sn (0.070–1.026 µg/g). Two-way ANOVA demonstrated significant effects of age, gender and age*gender interaction on hair metals in both cities. At the same time, the age-specific changes in hair metal content were more expressed in children from Novosibirsk, being exposed to higher metal pollution. The obtained data demonstrate that age, gender as well as the particular rate of pollution in each location should be taken into account during interpretation of hair test results. © 2018, © 2018 Informa UK Limited, trading as Taylor & Francis Group.