A method consisting of solvent extraction using hexane for defatting, multifunctional cleanup column, and HPLC determination was validated for the analysis of deoxynivalenol (DON) and zearalenone (ZEA) in wheat germ and wheat germ oil. A total of 36 batches of grain wheat were subjected to industrial milling and the distribution factors in milled germ were 47% for DON and 71% for ZEA. A survey of 50 samples of germ-based dietary supplements revealed that 60% of wheat germ and 40% of wheat germ oils contained DON at mean values of 111 and 41 μg/kg, respectively, while none of germ samples and 16% oils contained ZEA (mean 6 μg/kg). Contamination levels lead to a daily intake of 1.3 μg DON and 0.03 μg ZEA, representing 1.9% and 0.23% of their respective tolerable daily intakes (TDI).