Plant breeding with elite parents within closed populations has proven to be a successful strategy to achieve genetic gains and conserve favorable gene complexes. To investigate the effects of advanced cycle breeding on genetic gain, phenotypic variation, and germplasm differentiation, 15 agronomic and malting quality traits were evaluated for a set 98 genotypes including ancestors, parental founders, and elite breeding lines developed at the University of Minnesota barley (Hordeum vulgare L.) breeding program between 1958 and 1998. The material was evaluated in five trials at three locations in 2002 and 2003. Significant gains were observed for 11 traits during the 40-yr period of advanced cycle breeding, including yield, lodging, malt extract, and wort beta-glucan content. In parallel, we observed a change in phenotypic variance for seven traits while eight traits, including yield, showed no change. Of the seven traits that showed a change in variance, five showed a reduction, one increased, and one was variable.There were significant correlations among most of the traits, most likely due to simultaneous selection. A principal component analysis explaining 58.1% of the variation showed differentiation of the most recent breeding lines from the breeding program founders. Retrospective analysis of changes in genetic gain and phenotypic variance can be useful in designing strategies to manage genetic variation for target traits in breeding programs.