Food quality depends largely on the source of origin of the products used. Here we use methylation sensitive amplified polymorphisms (MSAP) analysis to diagnose and quantify the tissue of origin in salmon and veal products. We exploited the variability of MSAP profiles between tissues of an organism in order to characterise the origin of the food product. MSAP profiles provided robust discrimination of tissues from salmon (brain, eye, liver and muscle) and veal (heart, kidney, liver and muscle). Isolation of the diagnostic markers revealed by MSAP may ultimately allow for the development of a new STS-based epigenetic profiling technique for the detection and quantification of mixture of tissues in the same sample: offering not only rapid determination of the tissue of origin but also potential quantification of the components in processed food products. (C) 2011 Elsevier Ltd. All rights reserved.