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Boran cattle provide livelihood to thousands of households in the arid and semiarid lands of Kenya. Due to their superior adaptive and productive traits in comparison to other breeds of cattle, they have also become a popular choice for breeders in Eastern and Southern Africa. Continued genetic improvement of the breed is important, and therefore accurate performance and pedigree records are required. One hundred seventy-eight pedigree records and blood samples of four Boran stud herds were evaluated for accuracy of parentage allocation using 11 microsatellite markers recommended by ISAG for parentage verification. The panel of the 11 microsatellite markers was found to be highly polymorphic (PIC of 0.6901) with a combined probability of exclusion of 0.9997. The dam misidentification was low ranging between 0% and 5% for the herds tested. The estimated rate of mispaternity however ranged between 4.3% and 80% among the four stud herds, and more than 50% of the offspring of some herds were misidentified. The high rate of mispaternity will have a negative impact on the response to selection. The use of DNA markers for parentage assignment will improve the accuracy of the pedigree records of Boran stud cattle in Kenya and contribute to more accurate selection of superior animals.