Different breeds and types of horses are raised in different regions of Turkey. The numbers and types of native horses have declined steadily over time because of increased agricultural mechanization. The blood samples of 85 native Turkish horses of different types from different geographical regions (Kars-Erzurum 30, Sanliurfa 20 and Adapazari 35) were analysed for blood protein polymorphism. Starch gel electrophoresis, polyacrylamide gel electrophoresis and polyacrylamide isoelectric focusing were used to identify genotypic variants of albumin (ALB), transferrin (TF), hemoglobin alpha (HBA), vitamin D-binding protein (GC), serum carboxylesterase (ES), A1B-glycoprotein (A1B), 6-phosphogluconate dehyrogenase (6-PGD) and phosphoglucomutase (PGM) loci. The direct counting method was used to calculate the frequency of genes for blood protein systems. Homozygosity degrees and chi-square were calculated with the frequency of genes for blood protein systems. According to the results of chi-square testing on eight systems of three different regions, 6-PGD system was significant P<0.001 in the eastern population (Kars-Erzurum). Among the local horses in the south-east region (Sanliurfa) 6-PGD system (P<0.001) and HBA system (P<0.05) were found to be significant. On the other hand, in the western region (Adapazari), chi-square analyses of 6-PGD and HBA systems were found to be significant at P<0.05. In this study, it was found that the three different local horse types in the three regions descended from the same origin.