Finger or heel-pricked blood sampling for fatty acid analysis is suitable especially in newborn infants where blood sampling is difficult and phlebotomy for research can be unethical. The aim of this study was to evaluate dried blood long chain polyunsaturated fatty acids (LC-PUFA) stability during storage at −28 °C. We collected 12 blood cord samples that were analyzed immediately after blood drawing, with and without drying the blood on filter paper. Dried samples were then analyzed 7 days and 1, 3, and 6 months after collection. Butylated hydroxytoluene was added to all samples. Fatty acid composition and 13C enrichment were measured by gas chromatography and by gas chromatography-isotope ratio mass spectrometry, respectively. The fatty acid composition, expressed in mol%, of the major LC-PUFA at day 7 was not statistically different from time 0, however lower values were found by the first month of storage. The 13C enrichment of 20:4n-6 and 22:6n-3 did not differ during the whole study period. LC-PUFA analysis from dried umbilical cord blood in neonates should be performed within a week, major losses of LC-PUFA occur afterwards. However, fatty acids obtained from dried blood maintain their 13C enrichment value for up to 6 months and thus these samples are suitable for natural abundance isotopic studies.