Populations experience a continual input of new mutations with fitness effects ranging lethal to adaptive. While the distribution of fitness effects (DFE) of new mutations is not directly observable, many mutations likely have either no effect on organismal fitness or are deleterious. Historically, it has been hypothesized that populations carry many mildly deleterious variants as segregating variation, which may decrease the mean absolute fitness of the population. Recent advances in sequencing technology and sequence conservation-based metrics for predicting the functional effect of a variant permit examination of the persistence of deleterious variants in populations. The issue of segregating deleterious variation is particularly important for crop improvement, because the demographic history of domestication and breeding allows deleterious variants to persist and reach moderate frequency, potentially reducing crop productivity. In this study, we use exome resequencing of thirteen cultivated barley lines and genome resequencing of seven cultivated soybean lines to investigate the prevalence and genomic distribution of deleterious SNPs in the protein-coding regions of the genomes of two crops. We find that putatively deleterious SNPs are best identified with multiple prediction approaches, and that SNPs that cause protein truncation make up a minority of all putatively deleterious SNPs. We also report the implementation of a SNP annotation tool (BAD_Mutations) that makes use of a likelihood ratio test based on alignment of all currently publicly available Angiosperm genomes.