A highly significant quantitative trait locus (QTL) on pig chromosome 6, affecting intramuscular fat (IMF), has previously been detected by our group and others. Two genes of positional and biological interest, the small heterodimer partner (SHP; NR0B2) and the heart fatty acid binding protein (FABP3; H-FABP), were investigated for meat quality traits and IMF respectively. SHP was partially sequenced (GenBank: DQ002896 and DQ002897) and mapped to the QTL region on porcine chromosome 6, affecting IMF. The map shows no recombination between SHP and FABP3, which was previously mapped to the same QTL region. Twelve single nucleotide polymorphisms were detected in the sequenced region of SHP gene. Haplotype information was used to investigate association between genetic variation and different meat quality traits. SHP haplotype combinations were found to have significant effect on connective tissue. However, further studies are needed to evaluate this possible association more effectively. The FABP3 is involved in fatty acid transport and has been studied as a candidate gene for IMF by several research groups. In our study, FABP3 genotypes were confirmed to be significantly associated with IMF in pigs. The average content of IMF in our population was 1.6%, which may indicate that the FABP3 polymorphism explains as much as 30-35% of the variation in IMF in our pig cross-population.