A whole genome scan of Finnish Ayrshire was conducted to map quantitative traitloci (QTL) affecting milk production. The analysis included 12 half-sib familiescontaining a total of 494 bulls in a granddaughter design. The families weregenotyped with 150 markers to construct a 2764 cM (Haldane) male linkage map. Inthis study interval mapping with multiple-marker regression approach wasextended to analyse multiple chromosomes simultaneously. The method usesidentified QTL on other chromosomes as cofactors to increase mapping power. Theexistence of multiple QTL on the same linkage group was also analyzed by fittinga two-QTL model to the analysis. Empirical values for chromosome-wisesignificance thresholds were determined using a permutation test. Twogenome-wise significant QTL were identified when chromosomes were analyzedindividually, one affecting fat percentage on chromosome (BTA) 14 and anotheraffecting fat yield on BTA12. The cofactor analysis revealed in total 31genome-wise significant QTL. The result of two-QTL analysis suggests theexistence of two QTL for fat percentage on BTA3. In general, most of theidentified QTL confirm results from previous studies of Holstein-Friesiancattle. A new QTL for all yield components was identified on BTA12 in FinnishAyrshire.