Mycotoxins can find their way into the human food chain in a variety of ways and have been shown to be present in many different foods and animal feed products. These mycotoxins can cause a toxic response, termed a mycotoxicosis, if ingested by higher vertebrates and other animals. Many are known carcinogens and others have been shown to elicit a variety of different responses in humans upon ingestion including; deterioration of liver or kidney function together with neurotoxicological effects ranging from skin sensitivity to extreme immunodeficiency. In this paper, the production of two groups of mycotoxins, namely, the aflatoxins and ochratoxin A will be discussed together with the development of molecular based detection techniques to monitor mycotoxin production.