A review of main methodological questions regarding biomarkers is reported focusing on validation, laboratory variability, study design and statistical analysis. The indicated perspective is the setup of protocols finalized at the study of multiple panels of genotoxicity biomarkers taking into account the influence of gene-environment interaction at low doses, of the modulation of the biomarkers associated to the genetic polymorphism. An overview on the influence of metabolic and DNA repair polymorphisms on biological indicators of genotoxic risk in occupational, environmental or life-style exposure is also presented. Genetic polymorphisms that influence human genotoxic risk are those of glutathione s-transferase and cytochrome P450 in exposure to polycyclic aromatic hydrocarbons (PAHs), those of N-acetyltransferase in both occupational and environmental exposures to aromatic amines (AAs) and similar compounds. Lastly recent and important studies, on the effect of the newly discovered polymorphisms affecting DNA repair enzymes on the modulation of genotoxic risk linked to life style (i.e., aflatoxin and PAHs from diet) and smoking behaviour and to environmental genotoxic exposure, are reported. To date biomarkers represent a new tool for epidemiological research in occupational medicine and they could represent a valid instrument for group evaluation but they are not useful for the risk assessment on individual basis. To achieve this objective it is necessary to demonstrate a stronger association with the endpoint that perhaps the future development of genetic and molecular epidemiology will make possible.