Long noncoding RNAs (lncRNAs) are emerging as crucial regulators of gene expression in immune system. It has been reported that lncRNAs participate in regulation of immune responses through both transcriptional and post-transcriptional mechanisms. In this review, we summarize the molecular functions of lncRNAs and discuss their binding to DNA, RNA and protein targets. We focus on the regulatory function of lncRNAs in both innate and adaptive immunity, as well as in autoimmunity and cancer immunology. In addition, we point out the limitation in current knowledge and future directions for the study of lncRNAs in the immune system.