At the current rate of technological progress, high-throughput sequencing of nucleic acids has become a commodity. These techniques are perfectly suitable for viral small RNAs sequencing and contribute to the understanding of many aspects of virus biology in the context of host–pathogen interaction. However, the generation of high quality data is still an issue and the preparation of small RNAs libraries that accurately reflect the viral siRNAs in the sample remains a challenge. In this chapter we describe how to clone and sequence libraries of viral small RNAs from infected insect samples (mosquito, drosophilidae, insect-derived cell lines).