Diversity across plant and animal genomes is patterned by the combined effects of drift and natural selection. To better understand the role of these processes in domesticated organisms, we investigated diversity across the genomes of domesticated maize and its wild relative teosinte. We first show that there is little evidence of selection on beneficial amino acid substitutions, and that the domestication bottleneck led to a decline in the efficiency of purifying selection in maize. We then show that rapid expansion post-domestication dramatically changed this relationship, with stronger purifying selection in maize, reflecting the much larger effective size of present day populations. Finally, we resequenced a number of genomes of landrace maize to show the impacts of colonization and demography on the distribution of deleterious alleles in the maize genome.