MicroRNAs (miRNAs) are about 20-22 nucleotide conserved non-coding RNA molecules that post-transcriptionally regulate gene expression by targeting the 3'-untranslated region of specific messenger RNAs (mRNAs) for degradation or translational repression. During the last two decades, miRNAs have emerged as critical regulators of a range of biological processes including immune cell lineage commitment, differentiation, maturation, and immune signaling pathways. The endoribonucleases such as Dicer, which is required for miRNA biogenesis, has also been shown to play an important role in inflammatory response and autoimmunity. Thus, dysregulated miRNA expression patterns have been documented in a broad range of human diseases including inflammatory and autoimmune diseases. In this review, we will discuss recent advances in miRNAs mediated regulation of inflammatory responses and autoimmune pathogenesis. Specifically, we will discuss how miRNAs regulate autoimmunity through affecting the development, differentiation, and function of various cell types such as innate immune cells, adaptive immune cells and local resident cells. The identification of distinct miRNA expression patterns, and a comprehensive understanding of the roles of those dysregulated miRNAs in inflammatory autoimmune pathogenesis offers inspirations of not only potential molecular diagnostic markers but also novel therapeutic strategies for treating inflammatory autoimmune diseases.