High-throughput sequencing has allowed for a comprehensive small RNA (sRNA) expression analysis of numerous tissues in a diverse set of organisms. The computational analysis of the millions of generated sequencing reads has led to the discovery of novel miRNAs and other sRNA species, and resulted in a better understanding of the roles these sRNAs play in development and disease. This chapter describes the generation of sRNA deep-sequencing libraries for the Illumina massively parallel sequencing platform by using a cloning method that anneals specific RNA sequences to the 5′- and 3′-ends of the sRNA molecules.