In the present study, two strains of Aspergillus flavus (one from a human corneal ulcer and one from the environment) were found to be strikingly similar in vitro in terms of thermotolerance, inability to grow in an anaerobic environment and in secreting proteinases; however, one obvious difference was that the clinical isolate produced 120 ppb of aflatoxin B1 in glucose salt medium while the environmental isolate did not produce this toxic metabolite. Alterations in the activities of acid phosphatase (ACP), alkaline phosphatase (ALP), lactate dehydrogenase (LDH) and glutathione-S-transferase were observed in the liver, kidney and serum in an experimental rat model, irrespective of whether the animal had been challenged with the clinical isolate or the environmental isolate of A. flavus. In rats that had been challenged with the clinical isolate, a significant decrease in the activity of kidney ALP was noted, whereas in rats that had been challenged with the environmental isolate, the reverse was observed. While these differential alterations may have occurred due to differences in the toxin-producing ability of the two isolates, further investigation is warranted to clarify whether other phenotypic, or genotypic, differences are also involved.