The present study was carried out to evaluate and compare the status of infection and assessment of risk factors in 353 blood samples (144 cattle and 209 buffaloes) of bovines by PCR assay along with microscopic examinations (ME). ME revealed prevalence of Babesia bigemina and Trypanosoma evansi to be 22.91% and 0.69%, respectively in cattle and 12.44% and 0.95%, respectively in buffaloes. Conversely, PCR assay was able to detect 40.97% and 3.47 % prevalence of B. bigemina and T. evansi in cattle and 23.92% and 6.69% in buffaloes, respectively. The result revealed that the PCR assay was 100% sensitive and 82.9% specific when compared with ME for babesiosis and 100% sensitive and 95.42% specific for trypanosomosis. Multivariate logistic regression models showed that risk of babesiosis was significantly higher in cattle (Odds ratio (OR) =2.207, P=0.001) compared to buffaloes. The risk for surra in male buffaloes increased by 6.37 times (OR= 6.375, P=0.013). Conversely, risk of babesiosis was significantly lower in male cattle than females (OR= 0.467, P=0.044).