High-throughput sequencing techniques have been applied to the discovery of several different regulatory small RNAs, including siRNAs and microRNAs in different plant species. Their subsequent characterization demands the use of sensitive and quantitative methods for their detection. Here we describe the use of northern blot and quantitative PCR for these purposes. We highlight the advantages and shortcomings of each method and offer a detailed description of those techniques that best work in our hands, in particular having in mind their use for the study of several small RNAs in a given sample. We enumerate relevant alternatives as well as cautionary comments in cases where we have detected potential difficulties.