Rats were used as biological indicators of air quality in two heavily polluted Brazilian towns: São Paulo and Cubatão. They were exposed for 6 months to ambient air in areas where the pollution was known to be severe. The following parameters were studied and compared to those of control animals: respiratory mechanics, mucociliary transport, morphometry of respiratory epithelium and distal air spaces, and general morphological alterations. The results showed lesions of the distal and upper airways in rats exposed in Cubatão, whereas the animals from São Paulo showed only alterations of the upper airways but of greater intensity than those observed in the Cubatão group. There are both qualitative and quantitative differences in the pollutants of these places: in São Paulo automobile exhaust gases dominate and in Cubatão the pollution is due mainly to particulates of industrial sources. The correlation of the pathological findings with the pollutants is discussed and it is concluded that biological indicators are useful to monitor air pollutions which reached dangerous levels in São Paulo and Cubatão.