A cross-sectional study was conducted using 150 blood samples collected from apparently normal/healthy crossbred cattle of Northern Kerala, South India, for detection of haemoprotozoan infections using staining techniques (Giemsa and Acridine Orange) and specific PCR. Theileria like piroplasms and Babesia bigemina were the only protozoan organisms detected in blood smears. Polymerase chain reaction using specific primers revealed amplification of products specific for Trypanosoma evansi (34.6%), Theileria sp. other than T. annulata (16%) and B. bigemina (0.6%). The higher prevalence rate of Trypanosoma evansi indicated that the subclinical parasitism can be due to higher prevalence of tabanid flies. The study also revealed the presence of a theilerial piroplasm other than T. annulata in North Kerala, which needs further investigation.