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Abstract Background Chemotherapy is a principle tool for the control and prevention of piroplasmosis. The search for a new chemotherapy against Babesia and Theileria parasites has become increasingly urgent due to the toxic side effects of and developed resistance to the current drugs. Chalcones have attracted much attention due to their diverse biological activities. With the aim to discover new drugs and drug targets, in vitro and in vivo antibabesial activity of trans-chalcone (TC) and chalcone hydrate (CH) alone and combined with diminazene aceturate (DA), clofazimine (CF) and atovaquone (AQ) were investigated. Methodology/Principal findings The fluorescence-based assay was used for evaluating the inhibitory effect of TC and CH on five of Babesia and Theileria species, including B. bovis, B. bigemina, B. divergens, B. caballi, and T. equi, the combination with DA, CF, and AQ on in vitro cultures, and on the multiplication of a B. microti–infected mouse model. The cytotoxicity of compounds was tested on Madin– Darby bovine kidney (MDBK), mouse embryonic fibroblast (NIH/3T3), and human foreskin fibroblast (HFF) cell lines. The half maximal inhibitory concentration (IC50) values of TC and CH against B. bovis, B. bigemina, B. divergens, B. caballi, and T. equi were 69.6 ± 2.3, 33.3 ± 1.2, 64.8 ± 2.5, 18.9 ± 1.7, and 14.3 ± 1.6 µM and 138.4 ± 4.4, 60.9 ± 1.1, 82.3 ± 2.3, 27.9 ± 1.2, and 19.2 ± 1.5 µM, respectively. In toxicity assays, TC and CH affected the viability of MDBK, NIH/3T3, and HFF cell lines the with half maximum effective concentration (EC50) values of 293.9 ± 2.9, 434.4 ± 2.7, and 498 ± 3.1 µM and 252.7 ± 1.7, 406.3 ± 9.7, and 466 ± 5.7 µM, respectively. In the mouse experiment, TC reduced the peak parasitemia of B. microti by 71.8% when administered intraperitoneally at 25 mg/kg. Combination therapies of TC–diminazene aceturate and TC–clofazimine were more potent against B. microti infection in mice than their monotherapies. Conclusions/Significance In conclusion, both TC and CH inhibited the growth of Babesia and Theileria in vitro, and TC inhibited the growth of B. microti in vivo. Therefore, TC and CH could be candidates for the treatment of piroplasmosis after further studies. Author summary Protozoa of the genus Babesia are the second most common blood-borne parasites of mammals after the trypanosomes. Babesia and Theileria are the etiological agents of piroplasmosis, a tick-transmitted disease causing substantial losses of livestock and companion animals worldwide and has recently gained attention as one of the emerging zoonosis in humans. Diminazene aceturate and imidocarb dipropionate are still the first choices for the treatment of animals. However, these drugs cause many adverse effects. Furthermore, they are not approved for human medicine. Therefore, the development of alternative treatment remedies against babesiosis is urgently required. In the present study we evaluated the effects chalcone hydrate (CH) and trans-chalcone (TC), against the growth of four species of Babesia and T. equi. Furthermore, we studied the chemotherapeutic potential of TC on B. microti in mice. The effects of the combined treatment of TC with DA, CF and AQ revealed that TC was found to diminish the adverse effects of these drugs