To study zonation of liver gene expression, we obtained periportal or perivenous rat liver cell lysates virtually devoid of nuclear material by site-directed digitonin infusion in situ. Total RNA was isolated, messenger RNAs were reverse transcribed and complementary DNAs were assayed after polymerase chain reaction-mediated amplification. The zonal distribution of messenger RNAs of alcohol dehydrogenase (little zonation), glutamine synthetase (perivenous) and cytochrome P-450 2E1 (perivenous) messenger RNAs, as analyzed by this technique, were found to be similar to the distribution of corresponding apoproteins. Using appropriate primers or complementary DNAs, zonation of many different messenger RNAs can be determined from the same sample by this simple and rapid method.