The role of imprinting in body composition was investigated in an experimentalcross between Chinese Meishan pigs and commercial Dutch pigs. A whole-genomescan revealed significant evidence for five quantitative trait loci (QTL)affecting body composition, of which four were imprinted. Imprinting was testedwith a statistical model that separated the expression of paternally andmaternally inherited alleles. For back fat thickness, a paternally expressed QTLwas found on Sus scrofa chromosome 2 (SSC2), and a Mendelian-expressed QTL wasfound on SSC7. In the same region of SSC7, a maternally expressed QTL affectingmuscle depth was found. Chromosome 6 harbored a maternally expressed QTL on theshort arm and a paternally expressed QTL on the long arm, both affectingintramuscular fat content. The individual QTL explained from 2% up to 10% of thephenotypic variance. The known homologies to human and mouse did not revealpositional candidate genes. This study demonstrates that testing for imprintingshould become a standard procedure to unravel the genetic control ofmultifactorial traits.