In this study, a liquid chromatography/tandem mass spectrometry (LC-MS/MS) method was applied for the simultaneous detection and quantification of a broad spectrum of mycotoxins and fungal metabolites in domestic rice in Iran. A total of 20 fungal metabolites were detected in 65 rice samples. The result showed that all of the samples were contaminated to at least one mycotoxin. The most prevalent fungal metabolites were brevianamide F (81.5%), emodin (46.1%) and tryptophol (43.1%). The occurrence of aflatoxin B1 (AFB1), ochratoxin A (OTA), zearalenone (ZEN) and fumonisin B1 (FB1) was 21.5%, 4.6%, 29.2% and 9.2%, respectively. No detectable level of deoxynivelenol was found in any of the samples. The mean level of regulated mycotoxins was lower than the maximum limit. Co-occurrence of AF1-ZEN, ZEN-OTA and FB1-ZEN were observed in 4.6%, 3.1% and 4.6% of samples, respectively. This is the first report indicating the contamination of domestic rice in Iran with mycotoxins such as alternaria metabolites, citrinin, tryptophol and kojic acid.