The aim of this study was to trace selected nucleic acid and protein components of isogene versus Bt transgene maize within the bovine gastrointestinal tract (GIT). After feeding 22 cattle for 4 weeks with Bt176 maize, different plant genes and the recombinant protein CryIAb were quantified during digestion. Furthermore, a first initial characterization of rumen bacteria was approached, using 16rDNA gene sequencing comparing isogene- against transgene-fed animals. Ingesta samples of different GIT sections (rumen, abomasum, jejunum, colon) were analysed for chloroplast, maize invertase, zein and Bt toxin (CryIAb) gene fragments using quantitative real-time PCR. First, the initial gene dose of these maize genes was detected in maize silage. During digestion, a significant reduction of high-to-medium abundant plant gene fragments was shown depending on the dwell-time and the initial gene copy number. Immunoreactive CryIAb protein was quantified by ELISA in intestinal samples indicating a significant loss of that protein. Remarkable amounts of Bt toxin were found in all contents of the GIT and the protein was still present in faeces. For the first time, the influence of CryIAb transgene maize on rumen bacterial microflora was investigated compared to isogene material through analysis of 497 individual bacterial 16S rDNA sequences. In principle, specific bacterial leader-species could be identified in all bovine rumen extracts, but no significant influence of Bt176 maize feed was found on the composition of the microbial population. This investigation provides supplementing data to further evaluate the fate of novel recombinant material originating from transgene feed or food within the mammalian GIT.