Even though Hepatozoon spp. has been molecularly detected in several wild animals in Brazil, there is no report on the occurrence of Hepatozoon spp. DNA in bats in Brazil. This study aimed at detecting Hepatozoon, in addition to ectoparasites, in non-hematophagous bats sampled in central-western Brazil using blood smears, hematoxylin-eosin (HE)-staining liver/spleen preparations and molecular and phylogenetic techniques. A total of 135 spleen, 127 liver, and 133 blood samples were collected from 135 non-hematophagous bats from 12 different species in two different sites in Campo Grande, Mato Grosso do Sul state, in the Brazilian Cerrado region. Spleen and blood DNA samples were submitted to two conventional PCR protocols for Hepatozoon spp. based on 18S rRNA. No Hepatozoon spp. gamonts or meronts were observed in blood smears and HE-stained-liver preparations, respectively. While none of the spleen samples was positive for Hepatozoon spp. in the PCR assays, 5 (3 %) blood samples contained 18S rRNA Hepatozoon DNA, including 2/37 (5 %) Artibeus lituratus, 2/32 (6 %) A. planirostris, and 1/23 (4 %) Platyrrhinus lineatus. Out of 5 bats positive for Hepatozoon spp., 3 were parasitized by either Macronyssidae/Spinturnicidae mites or Streblidae flies. BLAST analysis showed that the sequences detected in bats had >99 % identity with Hepatozoon sequences detected in amphibians and reptiles from Brazil, including Hepatozoon caimani detected in Caiman crocodilus. The phylogenetic inferences estimated by the Maximum Likelihood and Bayesian methods clustered the Hepatozoon sequences detected in Brazilian bats with those detected in reptiles and amphibians.