For analysis of trace compounds, stable isotope dilution assays (SIDAs) have gained increasing importance in the past years. This methodology is based on the use of stable isotopically labelled analogues of the analytes as internal standards (IS). To take the mycotoxins patulin and ochratoxin A as examples, the benefits of SIDAs were demonstrated both for foods and for clinical analyses.Regarding PAT, an isotopomer labelled with(13)C was used as IS and enabled quantitation of the mycotoxin in tissues and blood. By applying this technology, a fast passive diffusion into tissue was proven with the model of the perfused rat stomach. Furthermore, rapid degradation of PAT was observed when it was reacted with blood, which was attributed to the formation of PAT-GSH adducts detected by LC-MS/MS.For OTA, a SIDA was based on the use of [(2)H5]-OTA as the IS and proved to be more accurate when compared to alternative methods such as HPLC-FD or ELISA. In contrast to PAT, OTA was detectable in human blood and urine samples. Under the assumption that the majority of OTA is circulating in blood, an urinary excretion rate of about 1% of the whole body content per day was calculated.