Autophagy is a highly conserved process by which defective organelles, non-functional proteins, and intracellular microorganisms become sequestered within structures called autophagosomes, which fuse with lysosomes and the engulfed components are degraded by lysosomal enzymes. In microbial autophagy degraded peptides are used to induce antigen-specific acquired immunity. Viruses, bacteria, fungi, and protozoa have developed strategies to subvert autophagy and/or to use this process to promote their replication and persistence. This review details the mechanisms by which microorganisms that infect the female genital tract and/or are detrimental to pregnancy interact with this host defence mechanism. Based on an understanding of autophagy-related pathological mechanisms, we propose new avenues for research to more effectively prevent and/or treat these infectious diseases.