In human populations, assortative mating is almost univer-sally positive, with similarities between partners for quantit-ative phenotypes 1-6, common disease risk 1,3,7-10, beha-vi-our 6,11, social factors 12-14 and personality 4,5,11. The causes and genetic consequences of assortative mating remain un-re-solved because partner similarity can arise from different mechanisms: Phenotypic assortment based on mate choice 15,16, partner interaction and convergence in phenotype over time 14,17, or social homogamy where individuals pair according to social or environmental background. Here, we present theory and an analytical approach to test for genetic evidence of assortative mating and find a correlation in genetic value among partners for a range of phenotypes. Across three independent samples of 24,662 spousal pairs in total, we infer a correlation at trait-associated loci between partners for height (0.200, 0.004 standard error, SE) that matched the phenotypic correlation (0.201, 0.004 SE), and a correlation at trait-associated loci for BMI (0.143, 0.007 SE) that was significantly lower than the phenotypic value (0.228, 0.004 SE). We extend our analysis to the UK Biobank study (7,780 pairs), finding evidence of a correlation at trait-associated loci for waist-to-hip ratio (0.101, 0.041 SE), systolic blood pressure (0.138, 0.064 SE) and educational attainment (0.654, 0.014 SE). Our results imply that mate choice, combined with widespread pleiotropy among traits, affects the genomic architecture of traits in humans.