Silage from a genetically modified potato expressing the 1-SST (sucurose:sucrose 1- fructosyltransferase) and the 1-FFT (fructan:fructan 1-fructosyltransferase) was used in a feeding experiment with pigs. After a feeding period of 42 days samples from various organs and digesta were collected and investigated with four different real time PCR systems, in order to identify the fate of the foreign DNA. No plant specific DNA or DNA specific for the genome alteration in the transgenic potato were detected in any organ. In contrast, chloroplast specific DNA was detected in the digesta of duodenum, jejunum, colon and rectum. The single-copy metallo-carboxypeptidase inhibitor gene sequence was detected only in samples from the stomach content of pigs fed the isogenic potato and in those from duodenum and jejunum of animals fed the transgenic one. No evidence for the integration of the foreign DNA into the host genome was observed.