T-2 and HT-2 toxins are secondary metabolites of various species of Fusarium. These molecules can have high potential toxic effects for human and animal health. In this work, ELISA and ultra performance liquid chromatography with fluorescence detection (UPLC/FLD) were implemented and validated as screening and confirmatory tests for the detection of these two toxins in cereal samples. The developed methods were tested by analyzing 100 samples of cereals by ELISA screening for reducing costs and analysis time and then using UPLC/FLD for confirmation purposes. Both methods met the performance criteria for sensitivity, linearity, selectivity, precision, and ruggedness, as reported in the European Decision No. 2002/657/EC and in Regulation (EC) No. 401/2006. The correlation between ELISA and UPLC/FLD approaches showed good results (r = 0.9056), confirming that these two techniques should be considered to be complementary in the official control activities of cereal and derived products.