The present study aimed to diagnose Babesia bigemina in naturally infected crossbred cows and to determine its effect on haemato-biochemical profile of host animals. Blood samples from lactating crossbred cows (n=30) between 3-6 years of age and showing clinical signs of babesiosis were collected, with or without anticoagulant, and analyzed for the protozoa by direct smear, direct blood PCR detection of the apical membrane antigen 1 (AMA-1) gene specific amplicon of B. bigemina and estimation of haematological and biochemical parameters. Healthy crossbred cows (n=10), examined free from haemoprotozoan infections were included as control. Blood Direct PCR revealed a 448-bp amplified fragment. Out of 150 random blood samples screened, (27/150) 18% were positive under light microscope, whereas direct blood PCR revealed (39/150) 26% samples positive for B. bigemina. The result shows higher specificity and sensitivity of PCR test over blood smear examination. The infected group showed significantly (p<0.001) decreased levels of TEC (3.04±0.19), Hb (4.78±0.27) and PCV (14.53 ±0.87) than healthy control animals. However, differences in the red blood cell indices (MCV, MCH and MCHC) were non-significant (p>0.05) between the groups indicating normocytic hypochromic anaemia in affected crossbred cattle. Serum samples of infected cows showed significantly (p<0.01) higher values of ALT (78.83±8.95), AST (146.13±7.62), BUN (27.09±1.02), creatinine (1.93±0.1) and TBIL (1.42±0.06) than that of healthy control. A significant decrease (p<0.01) of TSP (6.12±0.13) and albumin (2.39±0.09) was also recorded in the infected cows compare to healthy control. The standardized blood direct PCR method of the present investigation may be useful for rapid and reliable diagnosis of B. bigemina in conjunction with microscopic examination. Moreover, marked changes in haematological and serum biochemical profile observed in B. bigemina infected crossbred cows may be useful in understanding disease pathogenesis and undertaking necessary corrective measures.