While human gut microbiomes vary significantly in taxonomic composition, biological pathway abundance is surprisingly invariable across hosts. We hypothesized that healthy microbiomes appear functionally redundant due to factors that obscure differences in gene abundance across hosts. To account for these biases, we developed a powerful test of gene variability, applicable to shotgun metagenomes from any environment. Our analysis of healthy stool metagenomes reveals thousands of genes whose abundance differs significantly between people consistently across studies, including glycolytic enzymes, lipopolysaccharide biosynthetic genes, and secretion systems. Even housekeeping pathways contain a mix of variable and invariable genes, though most deeply conserved genes are significantly invariable. Variable genes tend to be associated with Proteobacteria, as opposed to taxa used to define enterotypes or the dominant phyla Bacteroidetes and Firmicutes. These results establish limits on functional redundancy and predict specific genes and taxa that may drive physiological differences between gut microbiomes.