miRBase is the primary online repository for microRNA sequences and annotations. The current release (miRBase 16) contains over 15,000 microRNA gene loci in over 140 species, and over 17,000 distinct mature microRNA sequences. Deep-sequencing technologies have significantly increased the rate of novel microRNA discovery. miRBase now maps reads from short RNA deep-sequencing experiments to microRNAs and provides web interfaces to view these mappings. Users can view all read data associated with a given microRNA annotation, filter reads by experiment and count, and search for microRNAs by tissue- and stage-specific expression. These data can be used as a proxy for relative expression levels of microRNA sequences, provide detailed evidence for microRNA annotations and alternative isoforms of mature microRNAs, and allow revisiting previous annotations. miRBase is available online at: http://www.mirbase.org/. miRBase was established in 2002 to provide microRNA researchers with stable and unique gene names for their novel microRNA discoveries and an archive of all microRNA sequences. The database has grown significantly, with the number of microRNA sequences in the database almost tripling in the last three years. The majority of the evidence supporting microRNA annotations now comes from deep-sequencing experiments. miRBase has developed an interface to view reads from RNA deep-sequencing data mapped to microRNA loci. The database also provides access to the primary evidence that supports microRNA annotations and links to microRNA target predictions and validations. The integration of deep-sequencing data into miRBase has been a major development. The database now includes data from human, Drosophila melanogaster, Arabidopsis thaliana, rice, and three nematode genomes. The database also provides several methods to access the sequence data, including browsing, sequence similarity, genomic coordinate intervals, keyword search, and bulk download. miRBase provides a clear picture of the profile of short RNAs generated from a microRNA locus, and facilitates the correction of errors and omissions in future releases. Deep-sequencing data aids in distinguishing microRNAs from other RNA species and fragments. Guidelines for microRNA annotation were established in 2003, requiring evidence of expression of a 22nt sequence and evidence for a microRNA precursor structure. Updated annotation criteria have been suggested to distinguish microRNAs from other classes of short RNAs in plants. The increased rates of microRNA detection afforded by deep-sequencing technologies provide challenges to the level of confidence required to annotate a sequence as a microRNA. The database is currently planned to expand to include microRNA candidates and predictions, and to develop a microRNA target aggregation service. miRBase is available online and free to all without restriction.miRBase is the primary online repository for microRNA sequences and annotations. The current release (miRBase 16) contains over 15,000 microRNA gene loci in over 140 species, and over 17,000 distinct mature microRNA sequences. Deep-sequencing technologies have significantly increased the rate of novel microRNA discovery. miRBase now maps reads from short RNA deep-sequencing experiments to microRNAs and provides web interfaces to view these mappings. Users can view all read data associated with a given microRNA annotation, filter reads by experiment and count, and search for microRNAs by tissue- and stage-specific expression. These data can be used as a proxy for relative expression levels of microRNA sequences, provide detailed evidence for microRNA annotations and alternative isoforms of mature microRNAs, and allow revisiting previous annotations. miRBase is available online at: http://www.mirbase.org/. miRBase was established in 2002 to provide microRNA researchers with stable and unique gene names for their novel microRNA discoveries and an archive of all microRNA sequences. The database has grown significantly, with the number of microRNA sequences in the database almost tripling in the last three years. The majority of the evidence supporting microRNA annotations now comes from deep-sequencing experiments. miRBase has developed an interface to view reads from RNA deep-sequencing data mapped to microRNA loci. The database also provides access to the primary evidence that supports microRNA annotations and links to microRNA target predictions and validations. The integration of deep-sequencing data into miRBase has been a major development. The database now includes data from human, Drosophila melanogaster, Arabidopsis thaliana, rice, and three nematode genomes. The database also provides several methods to access the sequence data, including browsing, sequence similarity, genomic coordinate intervals, keyword search, and bulk download. miRBase provides a clear picture of the profile of short RNAs generated from a microRNA locus, and facilitates the correction of errors and omissions in future releases. Deep-sequencing data aids in distinguishing microRNAs from other RNA species and fragments. Guidelines for microRNA annotation were established in 2003, requiring evidence of expression of a 22nt sequence and evidence for a microRNA precursor structure. Updated annotation criteria have been suggested to distinguish microRNAs from other classes of short RNAs in plants. The increased rates of microRNA detection afforded by deep-sequencing technologies provide challenges to the level of confidence required to annotate a sequence as a microRNA. The database is currently planned to expand to include microRNA candidates and predictions, and to develop a microRNA target aggregation service. miRBase is available online and free to all without restriction.