Noncoding RNAs (ncRNAs) are RNA molecules that do not undergo the process of translation into protein. High-throughput sequencing technology has shown that a large portion of the human genome is transcribed into ncRNAs. ncRNAs can be divided into different categories, including two main categories based on their size: microRNAs (miRNAs), which represent a subclass of endogenous small ncRNAs with an average 22 nucleotide length, and lncRNAs, which represent a subclass of ncRNAs over 200 nucleotides in length. Both of which have been identified in both mammalian and nonmammalian cells. miRNAs and lncRNAs are an essential part of the complex regulatory networks that control numerous biological processes and may play an important role in host defense and/or microbial offense during host–parasite interactions. Here, several methodologies to explore the role for miRNAs and lncRNAs in host–parasite interactions are briefly summarized, including the detection, quantification, and intracellular localization of miRNAs, identification and validation of miRNA targets, functional manipulation of specific miRNAs, mapping of lncRNA occupancy genome wide, and detection of the association between lncRNAs and proteins.