The mucosal barrier is composed of polarized epithelial cells with distinct apical and basolateral surfaces separated by tight junctions and serves as both a physical and immunological barrier to incoming pathogens. Specialized polarity proteins are critical for establishment and maintenance of polarity. Many human pathogens have evolved virulence mechanisms that target the polarity network to enhance binding, create replication niches, move through the barrier by transcytosis, or bypass the barrier by disrupting cell-cell junctions. This review summarizes recent advances and compares and contrasts how three important human pathogens that colonize mucosal surfaces, Pseudomonas aeruginosa, Helicobacter pylori, and Neisseria meningitidis, subvert the host cell polarization machinery during infection.