Background: Aflatoxins are well-known secondary metabolites of the mould Aspergillus flavus, but it is not clear whether aflatoxins are produced in tissues in the course of invasive aspergillosis due to aflatoxinogenic Aspergillus flavus strains. We sought to determine whether aflatoxin B1 is produced in tissues in experimental invasive aspergillosis due to aflatoxinogenic Aspergillus flavus. Methods: Corticosteroid-treated (immunosuppressed) Wistar rats received intravenous challenge with conidia from a known aflatoxin B1-producing strain of Aspergillus flavus (test rats) or with conidia from a aflatoxin non-producing strain of Aspergillus flavus (control rats). Animals were sacrificed after 10 days and key organs dissected out. Thin-layer chromatography was used to detect aflatoxin B1 in tissue homogenates; in addition, total protein concentration and protein profiles were determined. Histopathological studies were also done. Results: Aflatoxin B1 was detected in concentrations of 120 ppb and 70 ppb, respectively, in homogenates of liver and kidney of test rats, but was not detected in tissue homogenates from control rats. The total protein concentration as well as the protein profiles of homogenates of the liver, kidneys, eyes and spleen of test rats tended to show much greater alterations than those in control rats. Invasion of tissue by fungal hyphae tended to be more intense in test than in control rats, while the histoarchitecture of liver, kidney and spleen tissues underwent greater disruption in test than in control rats. Conclusions: Aflatoxin B1 is produced in tissues in experimental invasive aspergillosis due to aflatoxinogenic Aspergillus flavus and may account for the pronounced alterations in protein profiles and histoarchitecture compared to that occurring in invasive aspergillosis due to aflatoxin non-producing Aspergillus flavus.