A genome scan was conducted in two US Holstein half-sib families to identifyquantitative trait loci (QTL) affecting milk production and conformation traitsusing the granddaughter design. The sires of the two studied families wererelated as sire and son and had 96 and 212 sons respectively. A total of 221microsatellite loci were scored in both families. Statistical analysis wasperformed using two different analytical methods; half-sib least squaresregression and Bayesian Monte Carlo Markov Chain. Traits analysed included fivetraditional milk production traits, somatic cell count, daughter pregnancy rate,male fertility and 20 conformation traits. A total of 47 tests achieved at leastgenome-wise significance. However, results from the two methods of analysis wereonly concordant for QTL location and level of significance in eight instances.