As part of a survey on concentrations of radon, thoron and their decay products in different indoor environments of the Balkan region involving international collaboration, measurements were performed in 43 schools from 5 municipalities of the Republic of Macedonia. The time-integrated radon and thoron gas concentrations (C_Rn and C_Tn) were measured by CR-39 (placed in chambers with different diffusion barriers), whereas the equilibrium equivalent radon and thoron concentrations (EERC and EETC) were measured using direct radon–thoron progeny sensors consisting of LR-115 nuclear track detectors. The detectors were deployed at a distance of at least 0.5 m from the walls as well as far away from the windows and doors in order to obtain more representative samples of air from the breathing zone; detectors were exposed over a 3-month period (March–May 2012). The geometric mean (GM) values [and geometric standard deviations (GSDs)] of C_Rn, C_Tn, EERC and EETC were 76 (1.7), 12 (2.3), 27 (1.4) and 0.75 Bq m^-3(2.5), respectively. The equilibrium factors between radon and its decay products (F_Rn) and thoron and its decay products (F_Tn>^0.5m) were evaluated:F_Rn ranged between 0.10 and 0.84 and F_Tn>^0.5m ranged between 0.003 and 0.998 with GMs (and GSDs) equal to 0.36 (1.7) and 0.07 (3.4), respectively.