Fresh tomatoes, homegrown and from supermarkets, with developing fungal lesions were collected. Each lesion was sampled, and the resulting fungal cultures were identified morphologically and extracted for analyzes of secondary metabolites. The tomatoes were incubated at 25 C for a week, extracted, and analyzed for fungal metabolites. Extracts from pure cultures were compared with extracts from the moldy tomatoes and fungal metabolite standards in two HPLC systems with DAD and FLD detection. The results showed that Penicillium tularense, Stemphylium eturmiunum, and S. cf. lycopersici were postharvest spoilers of fresh tomatoes. The results also showed that P. tularense could produce janthitrems, paspalinine, paxilline, and 3-O-acetoxypaxilline, that S. cf. lycopersici could produce stemphols, and that S. eturmiunum could produce infectopyrone and macrosporin when grown in pure culture. This study is the first to report on the detection of tentoxin, paxillines, janthitrems, verrucolone, infectopyrone, macrosporin, and stemphols in naturally contaminated tomatoes.