The use of biomarkers in the Teplice Program, provided a key tool to relate health outcomes to individual personal exposures and to provide measures of confounding exposures. This research program on the health effects of air pollution studied a population living in the heavily industrialized district of Teplice in Northern Bohemia and compared the exposure and health of this population to that of a non-industrialized district, Prachatice, in Southern Bohemia. The studies included characterization of the environmental and personal air pollution exposure, biomarkers, and studies on reproductive, respiratory, and neurobehavioral effects. Biomarkers were measured in blood, urine, placenta, and sperm. The biomarkers included measures of exposure (e.g., urine metabolites and blood metals), dose (e.g., DNA adducts), DNA damage, genetic and cytogenetic effects, and susceptibility. During winter temperature inversions, unusually high concentrations of a complex mixture of air pollutants were measured, including fine particles, genotoxic organic compounds, and toxic trace elements. This population, however, was also exposed to multiple pollutants via all pathways, and including pollutants resulting from environmental exposures, occupational exposures, and personal habits (e.g., tobacco and alcohol use). Longitudinal and repeated measures used individuals as their own control to examine the influence of environmental exposures as they changed over time and season.