In renal allografts, assessing gene expression can add relevant diagnostic information to histopathology. Results can be expressed as single genes or gene sets, representing pathogenesis-based transcript sets (PBTs): cytotoxic T-cell-associated, interferon gamma- induced or decreased kidney parenchymal transcripts. Two technology platforms are available: RT-PCR and microarrays. We compared RT-PCR, U133plus2.0 microarrays and histopathology in 86 biopsies. We compared 13 potentially diagnostic genes as RT-PCR probes to microarray-derived PBTs, 'mini'-PBTs (small sets of 3-5 transcripts) and a histology classifier. Most RT-PCR probes (10/13) correlated well with the corresponding microarray probe sets (r > 0.8). Exceptions included FASLG and CD8B1 microarray probe sets, which were not performing on microarrays but were detectable by RT-PCR most likely due to differences in sensitivity. In general, RT-PCR showed greater dynamic range, detecting small changes in normal kidneys, but RT-PCR and microarrays gave similar results in abnormal kidneys. Individual transcripts or mini-PBTs assessed by either platform correlated well with one another, with microarray PBTs and the histology classifier. Thus, microarrays and RT-PCR assessments agree strongly with one another and histopathology in assessing transplant inflammation, particularly, when results are expressed as PBTs or mini-PBTs. The dynamic range of both platforms was sufficient to detect the relevant changes in rejection.