Kidney transplantation is often followed by disturbances of solute and volume maintenance. Rat kidney transplantation (NTX) models with or without acute rejection were used to analyze the molecular basis of these disturbances. Functional parameters showed that allogeneic NTX led to significant higher Na+ and urine volume excretion 4 days after NTX compared to control animals. Genexpression analysis of these kidneys using micro-arrays showed that several transport systems with significant importance for kidney functions were down regulated on the mRNA level compared to control kidneys. For example the aquaporins-1–4, the Na+/H+ exchanger Type 3, the epithelial Na+ channel and the Na+/glucose cotransporter were down regulated. These effects were not seen in syngeneically transplanted kidneys. Several regulatory factors with a positive influence on the regulation and expression of these proteins were also down regulated. This indicates that disturbances in renal transport function are due to complex effects of acute rejection on the expression and function of various renal transporters and their regulatory factors. This includes key transporters and channels for sodium and water.