Aflatoxins are secondary metabolites produced by the aflatoxigenic fungi in suitable conditions. Saffron, Crocus sativus, is the most expensive spice in the world. Saffron is normally contaminated with soil and hand microflora during harvest and post-harvest operations. In this study, rapid assessment of aflatoxigenic fungi in saffron was accomplished using polymerase chain reaction. In total, 37 market samples were assayed in order to isolate aflatoxin-producing fungi. The 18.9% of the total samples were contaminated with aflatoxigenic fungi. Our results also show that most of the isolated fungi were saprophytes which are normally originated from soil during harvest and postharvest process.