This study was carried out to determine the rate of Theileria infection in sheep and goats and identify the species by polymerase chain reaction (PCR). The prevalence of Theileria infection in sheep and goats was 33.75% and 28% respectively, by microscopical examination of blood smears from 80 sheep and 50 goats in Egypt. Five positive samples for Theileria infection were subjected to PCR using Theileria species specific primer. In addition, 5 negative samples for Theileria infection and apparently healthy were subjected to the same examination. Seven out of 10 blood samples (5 sheep and 2 goats) were PCR positive using Theileria species specific primer at 1098 bp. Three of those were PCR positive using T. ovis specific primer at 520 bp. T.
lestoquardi was detected in 3 samples by PCR at 230 bp. Two apparently healthy animals were positive for Theileria species PCR but negative for both T. lestoquardi and T. ovis. This indicated that, other nonpathogenic Theileria species may be present in Egypt. Only one sheep sample was showed mixed infection of both T. ovis and T. lestoquardi.