Ergot alkaloids and their epimer-specific determination have gained increasing importance for food safety. A solid-phase extraction and cleanup method based on sodium-neutralized strong cation exchange (Na(+)-SCX) was developed to quantitate 12 priority ergot alkaloids in rye flour and wheat germ oil by HPLC fluorescence analysis. Sample preparation is achieved by omitting acidic and alkaline conditions enabling minimized epimerization, which is necessary to determine ergot alkaloids according to their natural distribution in foods. Ergot alkaloids are eluted from SCX-column by forming ion pairs using a sodium hexanesulfonate containing solution which prevents epimerization for at least 96 h. Method validation yielded recoveries of 80-120% (rye flour) and 71-96% (wheat germ oil) with a maximum limit of quantitation (LOQ) of 2.0 μg kg(-1) per ergot alkaloid for both matrices. The applicability of the developed method was demonstrated by analyzing 16 samples from German retail markets: 9 rye flours (max 178 ± 5 μg kg(-1)) and, reported for the first time, 7 wheat germ oils (max 56.8 ± 2.7 μg kg(-1)) expressed as the sum of 12 ergot alkaloids.