The kidney plays a major role in excretory and reabsorptive processes. The kidney cortex consists primarily of proximal tubular cells, which are epithelial cells that are often involved in the induction and progression of various kidney diseases. Therefore primary proximal tubular cells are widely used as a renal cell model. To further characterize this kidney in vitro model different time points in culture after isolation of the cells were compared to the cortex in vivo using gene expression analysis based on microarrays. This study revealed that many metabolic pathways and some kidney-specific functions are lacking in the in vitro model. Furthermore genes involved in RNA and protein synthesis, intracellular transport, extracellular matrix and cytoskeletal organization were upregulated in culture compared to in vivo, indicating proliferation of the cells and differentiation into a cell culture phenotype. The data represented here may help to evaluate the in vivo relevance of results obtained with this in vitro model.