Methods for the screening of fungal cultures for toxic secondary metabolites are reviewed. Thin layer chromatography (TLC) and high-performance liquid chromatography (HPLC) are good general analytical methods for secondary metabolites in unpurified extracts. The combination of normal phase TLC using different chemical spray reagents with reversed phase HPLC, using alkylphenone retention indices and diode array detection, is a powerful technique for identifying the individual mycotoxins detected. The results of the screening methods are very dependent of the growth media and incubation conditions and a general method for the detection of Penicillium, Aspergillus, Fusarium, Alternaria and Cladosporium toxins is suggested.