The indoor and outdoor radon/thoron progenies concentrations and natural background radiation levels throughout Sarawak and Sabah were measured. The measurements were carried out at 234 locations in 40 towns in Sarawak and Sabah. The mean indoor and outdoor radon equilibrium equivalent concentrations (EEC) in Sarawak were found to be 1.2 Bqm-3 and 1.5 Bqm-3 respectively. In Sabah, the mean indoor and outdoor radon equilibrium equivalent concentrations were 1.7 Bqm-3. The mean indoor and outdoor thoron equilibrium equivalent concentrations of 0.4 Bqm-3 and 0.3Bqm-3 respectively, were the same for Sarawak and Sabah. The mean indoor and outdoor radiation levels of 46 nGyh-1 and 42 nGyh-1 in Sarawak were slightly lower than the respective values in Sabah, i.e. 53 nGyh-1 and 46 nGy h-1.