The next generation sequencing technologies have made the exhaustive sequencing of all small RNA species within a small RNA library possible. Thus, comparative studies on the changes in small-RNA transcriptomes between two biological samples represent a powerful means of revealing the functions of small RNAs in physiological and pathological processes. Here, we describe a small RNA cloning method that can be used to generate small RNA cDNA libraries for both conventional and next generation (deep) sequencing. It can also be used for detection and quantitative analyses of small RNAs using PCR.