High-throughput n-3 fatty acid profiling is enabled by collection techniques such as venous whole blood and fingertip prick (FTP) sampling, but the resulting increased sample numbers increases storage demand. Highly unsaturated fatty acids (HUFA) in erythrocytes are susceptible to oxidation, but this tendency is poorly characterized in venous and FTP whole blood. Presently, whole blood samples with low and high n-3 content collected with ethylenediaminetetraacetic acid were stored on chromatography paper with and without BHT pre-treatment for up to 180 days at different temperatures (room, 4, -20, -75 °C). Whole blood prepared with heparin and BHT and stored in cryovials was also examined. Eicosapentaenoic acid (EPA, 20:5n-3) + docosahexaenoic acid (DHA, 22:6n-3) is relatively stable when stored at -75 °C under various conditions but rapidly decreases in whole blood when stored at -20 °C. At -20 °C, BHT + heparin prepared whole blood can prevent decreases in cryovials up to 180 days but BHT only slows the decreases on chromatography paper. Surprisingly, whole blood stored at 4 °C and room temperature was less susceptible to decreases in EPA + DHA as compared with -20 °C storage. Assessments of n-3 blood biomarkers indicate the % n-3 HUFA in total HUFA was more stable as compared with the sum of the relative % of EPA + DHA. In conclusion, FTP and venous whole blood for fatty acid analysis should be stored at -75 °C whenever possible. In the absence of -75 °C storage conditions, BHT should be added and 4 °C or room temperature appear to be better alternatives to -20 °C.