The genetic relevance of Turkish sheep has recently been revealed by mtDNA analysis, which has led to the identification of a third maternal lineage in that species. We present here a study of the genetic variation of these breeds at a nuclear level from the analysis of 30 microsatellite loci. Parameters of variability indicated a high level of variation in the breeds analysed. Mean number of alleles per locus ranged from 7.8 to 10.4 and gene diversity varied between 0.69 and 0.74. Considerable differences were detected between breeds regarding the pattern of within-breed variability. Breed-specific alleles were detected at most loci and all breeds analysed, a total of 75 private variants being identified. The Hemsin sheep showed noticeably lower genetic variation in accordance with the present status of this breed. Percentages of shared alleles (from 54.8% to 69.5%) and gene flow estimates (from 5.98 to 28.32) gave information about the relative genetic differentiation of breeds. The results presented here for nuclear DNA complement those reported for mtDNA and bear out the need to preserve this invaluable genetic material.