The aim of this study was to 1) detect QTL across the cattle genome that influence the incidence of clinical mastitis and somatic cell score (SCS) in Danish Holsteins, and 2) characterize these QTL for pleiotropy versus multiple linked quantitative trait loci (QTL) when chromosomal regions affecting clinical mastitis were also affecting other traits in the Danish udder health index or milk production traits. The chromosomes were scanned using a granddaughter design where markers were typed for 19 to 34 grandsire families and 1,373 to 2,042 sons. A total of 356 microsatellites covering all 29 autosomes were used in the scan. Among the across-family regression analyses, 16 showed chromosome-wide significance for the primary traits incidence of clinical mastitis in first (CM1), second (CM2), and third (CM3) lactations, and SCS. Regions of chromosomes 5, 6, 9, 11, 15, and 26 were found to affect CM and regions of chromosomes 5, 6, 8, 13, 22, 23, 24, and 25 affected SCS. Markers on chromosomes 6, 11, 15, and 26 can be used to perform marker-assisted selection on CM without a direct negative selection on milk yield, because no effects were detected on the milk traits. Comparing multi-trait models assuming either a pleiotropic QTL affecting 2 traits or 2 QTL each affecting 1 trait gave some evidence to distinguish between these models. For Bos taurus autosome 5, the most likely models were a pleiotropic QTL affecting CM2, CM3, and SCS, and a linked QTL affecting fat yield index. For Bos taurus autosome 9, the most likely model is a pleiotropic QTL affecting CM1 and CM2 at approximately 8 cM.