The immune system senses exogenous threats or endogenous stress through specialized machinery known as pattern recognition receptors (PRRs). These receptors recognize conserved molecular structures and initiate downstream signaling pathways to control immune responses. Although various immunologic pathways mediated by PRRs have been described, recent studies have demonstrated a link between PRRs and autophagy. Autophagy is a specialized biological process involved in maintaining homeostasis through the degradation of long-lived cellular proteins and organelles. In addition to this fundamental function, autophagy plays important roles in various immunologic processes. In this review, we focus on the reciprocal influences of PRRs and autophagy in modulating innate immune responses.