Comparative genomics facilitates the identification of conserved and potentially functional elements. Their polymorphism can be responsible for phenotype variability. Two chromosomal regions were studied - one containing the FABP gene cluster and the second harbouring the FABP3 locus. Several highly conserved elements across four species (human, mouse, dog and cattle) were found, two of them were selected for association studies in the pig (the FABP4 enhancer and a fragment of intron 2 of the FABP3 gene). Four single nucleotide polymorphisms in the FABP4 enhancer sequence were found: 9 T/G, 31 C/G, 186 G/A, and 189 C/A. One of them (9T/G) was tested but the statistical analysis revealed no association with fatness traits in Polish Large White and Polish Landrace pigs. These studies demonstrate an integrated approach to identify, classify and select target DNA sequences for further association studies.