We measured V/Q distributions with the multiple inert gas elimination technique in five anesthetized artificially ventilated American alligators at 24 degrees C. The overall V/Q was relatively high (2.0 to 7.2) because of continuous artificial ventilation. The V/Q distributions were usually unimodal (log standard deviation of Q distribution averaged 0.47 +/- 0.09 [SD] and there was considerable shunt (28.5 +/- 10.3% of cardiac output). The data are consistent with a pulmonary, rather than central cardiovascular shunt. We also detected a molecular weight dependent limitation to inert gas elimination. The difference in error of fit to enflurane and cyclopropane retentions was significantly greater than predicted from experimental error. The estimated stratification diffusing capacity, a measure of this limitation, was 10% of the value estimated for mammals and similar to morphometric estimates of membrane diffusing capacity in alligators, which is comparatively low. Hence, even though the multicameral lungs of alligators are unevenly partitioned and have large gas phase diffusion spaces, V/Q matching and molecular weight dependent limitations are relatively small. Shunt, dead space and membrane diffusion resistances can be more important limitations of gas exchange.