The present study reports on the natural mycobiota occurring in cocoa beans, paying special attention to the incidence of fungal species that are potential producers of mycotoxins. The results show that predominant fungi were different species of the genus Aspergillus belonging to section Flavi and Nigri. Of the 214 strains of Aspergillus section Flavi collected from cocoa beans, 120 were identified as A. flavus and 94 as A. tamarii. Of Aspergillus section Nigri 138 strains were isolated, with 132 belonging to A. niger aggregate and 6 to A. carbonarius species. Potential ability to produce aflatoxins (AFs) B1, B2, G1 and G2, cyclopiazonic acid (CPA) and ochratoxin A (OTA) was studied by isolate culture followed by HPLC analysis of these mycotoxins in the culture extracts. Results indicated that 64.1% and 34.2% of the A. flavus strains produced AFs and CPA, respectively. Most of the A. flavus strains presented moderate toxigenicity with mean levels of AFs ranging from 100 ng g(-1) to 1000 ng g(-1). All the CPA-producing strains of A. flavus were highly toxigenic producing >30 microg g(-1) of CPA. Furthermore, 98% of A. tamarii strains produced CPA and over 50% of them were highly CPA toxigenic. With respect to OTA-producing fungi, a high percentage of black aspergilli strains (49.2%) were able to produce OTA. Additionally, most of the OTA-producing isolates were of moderate toxigenicity, producing amounts of OTA from 10 microg g(-1) to 100 microg g(-1). These results indicate that there is a possible risk factor posed by AFs, CPA and OTA contamination of cocoa beans, and consequently, cocoa products.