microRNAs (miRNAs) represent a class of noncoding RNA species, believed to be regulating gene expression by binding to complementary sites in the 3'UTRs of target mRNAs. They play important regulatory roles in various metabolic pathways in most eukaryotes. The recent discovery of virus encoded miRNAs suggests that viruses may be using them to regulate host and viral gene expression. Another class of closely related small interfering RNAs (siRNAs) also has been found within the HIV-1 genome and shown to be exerting a limited impact on virus reproduction. Additionally, an additional type of viral noncoding RNAs named small noncoding RNAs (sncRNAs) ranging from a few tens to a few hundred nucleotides in length, has also been identified. sncRNAs have a wide phylogenesis and high levels of expression, suggesting they may play an important roles in different species. Here we discuss the genomic organization, expression, conservation as well as potential function of virally encoded miRNA, siRNA, and sncRNAs.