The widespread mycotoxins contamination of food commodities has made the monitoring of their levels essential. To overcome the disadvantages of the indirect approach by food analysis, detection of mycotoxin as biomarkers in urine provides a useful and specific data for exposure assessment to these food contaminants. In this work, a sensitive, rapid and accurate method based on gas chromatography-tandem mass spectrometry procedure to determine 15 mycotoxins and metabolites in human urine was optimized and validated taking into consideration the guidelines specified in Commission Decision 2002/657/EC and 401/2006/EC. A salting-out assisted acetonitrile-based extraction was used for sample preparation. The extraction recoveries were in a range of 72–109%, with intra-day relative standard deviation and inter-day relative standard deviation lower than 10% and 13%, respectively for all mycotoxins at 50, 100 and 200 µg/L spiking levels. The limits of quantitation ranged from 0.25 to 8 µg/L. Matrix effect was evaluated and matrix-matched calibration was used for quantitation. The proposed procedure was applied to 10 urine samples collected from children. Mycotoxins were quantified in 30% of samples.