Objective To develop an analytical method for determination of masked fumonisins in cereals by isotope dilution-ultra high performance liquid chromatography-tandem mass spectrometry. Methods The samples were extracted and diluted for determination of parental fumonisins. Another portion of extracted samples were alkaline hydrolyzed and cleaned up using strong anionic exchange adsorbent (MAX) for determination of hydrolyzed fumonisins. The chromatographic separation was performed on a CORTECS C18 column (2.1 mm×100 mm, 1.6 μm) using 0.2% formic acid aqueous solution and methanol with 0.2% formic acid as the mobile phase under gradient elution. The six fumonisins of FB1, FB2, FB3, HFB1, HFB2 and HFB3 were analyzed by tandem mass spectrometry using multiple reactions monitoring (MRM) mode. The isotope dilution method was applied for quantitative analysis. Results The six fumonisins showed good linearity with relative coefficients above 0.99. Limits of quantitation (LOQs) were in the range of 5.0-10 μg/kg. At the low, medium and high-spiked levels, the recoveries of fumonisins in three types of cereals were from 88.01% to 114.21%, with precision (RSD) of 0.72%-11.5%. Conclusion This method is accurate, sensitive and reproducible for the determination of masked fumonisins in cereals. It is suitable for the routine test in analytical chemistry laboratories for monitoring masked fumonisins levels in cereals.