In this study, several polymorphisms in the gene encoding the inducible form of the cytoplasmic Hsp90 (HSP90AA1) were characterized in 10 sheep breeds reared in different climatic regions of Turkey. A new indel (AA) polymorphism located at the -704 position in the HSP90AA1 5' flanking region was found in all investigated breeds. This polymorphism create/remove a GR transcription site that could affect heat stress response and is completely linked with the C/G transversion located at -660 in the same region of the gene. Genotype frequencies differed significantly between breeds. No clearcut relationship was found between this polymorphism and climate factors, but breeds from northern Turkey had higher frequencies of the indel AA allele than breeds from southern Turkey. (C) 2012 Elsevier B.V. All rights reserved.