Small RNAs such as small interfering RNAs (siRNAs) and microRNAs (miRNAs) play crucial roles in establishing general host defense mechanisms against viral infections in plants and the development of disease symptoms. Understanding these fundamental processes requires the sensitive and specific detection of small RNA species. However, because of the small size of miRNAs and siRNAs, their detection is technically demanding. Here, we describe methods for robust and sensitive detection of small RNAs by Northern blot analysis and in situ hybridization.