This paper presents a comprehensive overview of the published literature on microsatellites studied in cetaceans from 1989 to 2007. We inventoried 246 loci isolated from 18 and amplified in 51 cetacean species representing 11 families. The majority of loci (68%) were dinucleotide (CA) repeats, which were also shown to be on average more variable than tetranucleotide repeats. For each of these loci and the 1610 locus/species combinations, we present the species in which the markers were isolated and tested, specific diversity parameters (number of alleles, expected and observed heterozygosities), together with the primer sequences, the size range of the PCR products and the GenBank accession number. Simple analyses were performed on the assembled data and the widespread use of cross-species amplification, an important source of microsatellites in cetaceans, is discussed using laboratory data from Stenella coeruleoalba. No significant ascertainment bias was detected when considering all dinucleotide or tetranucleotide loci. This comprehensive database should help to inform those working on population and conservation genetic studies in most cetacean species.