The field study was undertaken between 2010 to 2013 by joint research team of Ecohealth Alliances and ICDDR’B and laboratory work was done during the period of June, 2013 to February, 2014 in Pharmacology laboratory of Chittagong Veterinary and Animal Sciences University (CVASU), Chittagong, Bangladesh to find out the prevalence of haemo-protoza in blood smears of fruit and small bats. Giemsa was used to stain the pre-prepared slides and emulsion oil was used to visualize the protozoa under microscope. A total of 350 blood smears were included in the study and the prevalence of Babesia and Plasmodium were 2.65%, 2.32%, and 6.25%, 0%, respectively in fruit bats (Pteropus giganteus) and small bats (Megaderma lyra). The highest prevelence of Babesia was found in Khagrachari (6.90%) and lowest in Chakaria (0), Dinajpur (0) and Ramnagar (0) but the highest prevelence of Plasmodium was found in Faridpur (4.76%) and lowest in Khagrachari (0), Rangpur (0), Chakaria (0) and Dinajpur (0). The prevalence in both fruit and small bat were found no significant (p>0.05) variation. It is necessary to conduct more research on haemoparasties of bats due to public health concern.