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A whole genome scan of Finnish Ayrshire was conducted tomap quantitative trait loci (QTL) affecting milk production. The analysis included 12 half-sib families containing a total of 494 bulls in a granddaughter design. The families were genotyped with 150 markers to construct a 2764 cM (Haldane) male linkage map. In this study interval mapping with multiple-marker regression approach was extended to analyse multiple chromosomes simultaneously. The method uses identified QTL on other chromosomes as cofactors to increase mapping power. The existence of multiple QTL on the same linkage group was also analyzed by fitting a two-QTL model to the analysis. Empirical values for chromosome-wise significance thresholds were determined using a permutation test. Two genome-wise significant QTL were identified when chromosomes were analyzed individually, one affecting fat percentage on chromosome (BTA) 14 and another affecting fat yield on BTA12. The cofactor analysis revealed in total 31 genome-wise significant QTL. The result of two-QTL analysis suggests the existence of two QTL for fat percentage on BTA3. In general, most of the identified QTL confirm results from previous studies of Holstein-Friesian cattle. A new QTL for all yield components was identified on BTA12 in Finnish Ayrshire.