For evaluation of the suitability of Amplified Fragment Length Polymorphism(AFLP) for detection of quantitative trait loci in farm animals, a combinationof AFLP and selective genotyping has been applied as a rapid screening methodfor marker-QTL associations. Focusing on loci affecting eye muscle area, sixextreme discordant sib pairs were selected from a Duroc x Berlin Miniature PigF2 experimental cross and examined by using 48 AFLP primer combinations. Twoprominent AFLP markers were converted into simple codominant PCR markers (STS-Bo1 and STS-Bo3) and assigned to Sscr4 by physical and linkage mapping.Single marker analysis indicated association of the STS markers with a putativeQTL influencing eye muscle area. Interval mapping confirmed the presence of asignificant QTL for eye muscle area (Pgenomewide < 0.01) on the Sscr4, withSTS-Bo1 being the closer marker. At the same location, significant effects(Pgenomewide < 0.01) on carcass length and backfat thickness were also detected.Our results demonstrate the capability of the combination of AFLP analysis andselective genotyping as a method for detection of genome regions containing QTLin livestock.