The expression of cyclooxygenase (Cox)-1 and -2 mRNA was studied in tissues of Fisher 344 (F344) (n=3) and Brown Norway (BN) (n=3) strain rats using the reverse transcription polymerase chain reaction. Cox-1 mRNA was expressed in the liver, kidney and lung, but not in the heart. Cox-2 mRNA was expressed in the kidney, heart and lung, but not in the liver. The present results showed the differential expression of basal Cox-1 and Cox-2 mRNA in the rat tissues, suggesting that Cox-1 and Cox-2 may contribute to the regulation of normal pathophysiological conditions in a tissue-specific manner. Thus, it is desirable to perform mapping of the basal expression of Cox-1 and Cox-2 in specific organs in the body in order to anticipate the effects of non-steroidal anti-inflammatory drugs on normal pathophysiological conditions. Finally, no difference was observed between F344 and BN rat tissues in the levels of Cox-1 and Cox-2 mRNA expression.