Small RNAs regulate gene expression in many cellular processes. Emerging evidence suggests that host endogenous small RNAs and host RNA-silencing machinery represent a fundamental layer of control in plant immune responses. Pathogen-responsive endogenous small RNAs regulate gene expression reprogramming and fine-tuning in plant immune responses. Here we discuss the function of endogenous small RNAs, including microRNAs (miRNAs), small interfering RNAs (siRNAs), and long siRNAs (lsiRNAs), in plant immune responses and the strategies that pathogens have acquired to suppress host small-RNA pathways. Host endogenous small RNAs and small-RNA pathways play an important role in the plant immune responses to pathogen challenges.