Tissue availability of polyunsaturated fatty acids (PUFAs) is of major relevance for health, and it depends on both dietary intake and metabolic turnover. We found close associations between variants in the human genes of Δ5- and Δ6-desaturase, FADS1 and FADS2, and serum phospholipid contents of PUFAs and long-chain PUFAs (LCPUFAs). Polymorphisms and reconstructed haplotypes of FADS1 and the upstream region of FADS2 showed strong associations with levels of the n-6 LC-PUFA arachidonic acid (20:4n-6). Carriers of the less common polymorphisms and their respective haplotypes also had a lower prevalence of allergic rhinitis and atopic eczema. Our data demonstrate for the first time that the fatty acid composition of serum phospholipids is genetically controlled by the FADS1 FADS2 gene cluster. The investigated single nucleotide polymorphisms in this cluster explain 28% of the variance of serum phospholipid arachidonic acid and up to 12% of its precursor acids. Based on this genetic variation, individuals may require different amounts of dietary PUFAs or LC-PUFAs to achieve comparable biological effects. We strongly recommend including analyses of FADS1 and FADS2 polymorphism in future cohort and intervention studies addressing the biological effects of PUFAs and LC-PUFAs, which should enhance the sensitivity and precision of such studies.