Milk components originating from blood plasma substrates are synthesized in epithelial cells of the mammary gland. Milk lipids are synthesized from fatty acids which bind to specific proteins – FABPs (fatty acid binding proteins). FABPs are a family of small cytoplasmic proteins; nine members of the family have been identified so far (FABP1–FABP9) (Chmurzyńska et al., 2006). Their main roles include fatty acid uptake, transport and metabolism. FABPs can modulate the fatty acid concentration in cells and therefore they affect different cellular processes, especially lipid metabolism. FABP3 and FABP4 are present in tissues with a high demand for fatty acids, such as heart muscle, skeletal muscles, lactating mammary gland, liver or adipose tissue (Roy et al., 2003). FABP3 gene was mapped to bovine chromosome 2 (Calvo et al., 2004), where QTLs affecting milk fat yield and content were described (Khatkar et al., 2004). FABP4 gene was mapped to BTA14 (Michal et al., 2006), which is very rich in QTLs for milk production traits (Khatkar et al., 2004). Fatty acid transport is assisted by the specific proteins called FATPs (fatty acid transport proteins). This protein group includes SLC27A3 (solute carrier family 27, member 3). It belongs to the family of proteins that facilitate long-chain fatty acid transport across the cytoplasmic membrane. Another protein with similar functions is ANXA9 (annexin A9), the member of Ca2+ and phospholipid-binding protein family (Calvo et al., 2006b). Genes encoding SLC27A3 and ANXA9 were mapped to chromosome 3, within the region where QTLs for milk fat content and the other milk traits have been mapped. Both of the above-mentioned genes are expressed in the mammary gland (Calvo et al., 2006b). The polymorphic sites (SNPs – single nucleotide polymorphisms) within the bovine FABP3, FABP4, SLC27A3 and ANXA9 genes were identified (Wu et al., 2005; Calvo et al., 2006b; Michal et al., 2006; Cho et al., 2008). Associations between SNPs in these genes and milk production traits in cattle have not been reported so far. However, polymorphism in the FABP4 gene has been significantly associated with carcass traits in cattle (Michal et al., 2006; Cho et al., 2008). Due to their expression sites, physiological properties and chromosomal localisation, the described genes might be considered as candidate genes for milk production traits. The aim of this study was to determine allele and genotype frequencies and to establish possible associations between the ANXA9, SLC27A3, FABP3 and FABP4 SNPs, and selected milk traits in Jersey cows.