The use of biological markers as part of the efforts to detect early signs of environmentally related adverse effects was discussed. Pulmonary function tests themselves have been classic examples of biological markers used in this field for a long period of time. Issues of standardization, unreliability and inaccuracy took decades to be resolved for pulmonary function tests. The use of biomarkers to assess lung disorders has become just part of the various tools the clinician has at his disposal. A framework for assessing and describing biological markers was presented. It was a two dimensional matrix showing on one axis the types of biological markers and on the other the type of study designs and uses. The ordinate of the matrix showed the progression of study designs such as laboratory, transitional, etiologic, and public health applications. Several examples were given of the use of biomarkers in the study of malignant and nonmalignant lung diseases. These examples included polycyclic aromatic hydrocarbon/DNA adducts which have been found at greater levels in lymphocyte DNA of smokers, a polymorphism of glutathione-S-transferase which is a susceptibility marker in nonsmall cell lung cancer, CYP2D6 and DNA repair enzyme polymorphism, and the role of antioxidant enzymes, tumor necrosis factor and serum type-III procollagen peptide in coal dust induced lung disorders.