Since the dawn of civilization, humans have feared the unknown risks associated with the use of new natural herbs or other natural medications to cure their pain, aches and illnesses. In the ancient Indian Ayurvedic Medicine which is over 4000 years old, the 'Visha (poison) Tantra (wisdom)' was developed as a discipline of medicine encompassing Toxicology and Preventive Medicines. Visha Tantra included the study of various toxic herbs and animals and their antidotes as well as the biomarkers of toxic effects. In the Visha Tantra and the practice of Ayurvedic medicine, there have been objective descriptions of the changes in colour and amount of urine, changes in the colour of nails, skin, and eyes, breathing patterns, gastrointestinal disturbances, and precautionary measures to prevent adverse effects as biomarkers of toxicity associated with the use of herbal medicines and certain foods. The adverse effects are the inevitable outcome of the environmental and industrial chemicals and pharmaceuticals; however, efforts are ongoing to prevent unexpected life-threatening toxicities and / or irreversible organ damage. The search for non-invasive biomarkers that can be objectively linked to adverse effects associated with man-made synthetic chemicals including pharmaceuticals and environmental pollutants is becoming an important priority for academics, federal agencies, pharmaceutical and industrial companies. This publication is devoted to toxicity biomarkers of target organs of toxicity and molecular epidemiology. It provides a comprehensive review of a wide spectrum of biomarkers, including molecular epidemiology biomarkers of aflatoxin and hepatitis B virus induced hepatocarcinogenesis, cytokines as the biomarkers of hepatocellular injury, drug-induced vascular injury, nephrotoxicity and reproductive toxicity biomarkers.