Oriental theileriosis caused by Theileria orientalis is a growing health concern of lactating cows in its endemic areas. Rapid and sensitive diagnostic tests are demand areas for appropriate and effective prophylactic and therapeutic measures. Quantitative polymerase chain reaction (qPCR) is the answer for both detection and quantification of parasites. Present study deals with qPCR for detection of parasitemia level of T. orientalis in apparently healthy and clinically affected cows. Major piroplasm surface protein (MPSP) gene present in T. orientalis was cloned in pUC57 vector and transformed into E. coli Top 10 cells. Single and mixed infections of hemoprotozoa other than T. orientalis, causing anemia were differentiated through blood smear examination and PCR tests. T. orientalis was detected in 108 (63.15%) ill and 48 (26.66%) healthy cows. Piroplasms detected per 1000 red blood cells (RBCs) was 0-1 in the healthy group as compared to 3-22 in those showing clinical signs. Parasitemia in ill cows ranged between 6.9 × 102 and 4.5 × 103 parasites / µl of blood which was significantly higher (p<0.05) than healthy group (2.6 × 102 - 5.7 × 102 parasites / µl of blood). Phylogenetic study of the isolates showed similarity with Buffeli type that unfolded its pathogenic form in apparently healthy and ill cows.