In Brazil, canine hepatozoonosis is a tick-borne subclinical hemoparasitosis caused by a protozoa Hepatozoon canis and is highly prevalent in dogs in rural areas. An epizootiological study was conducted to investigate the prevalence of H. canis in the canine population of Ituberá, Bahia, and to analyze any associated risk factors. Blood samples were collected from 380 dogs and determined the presence of the protozoan by performing capillary blood smear and polymerase chain reaction (PCR). Epizootiological data were collected by asking dog owners to answer a structured questionnaire. H. canis gamonts were not detected in the blood smears. However, PCR detected H. canis in 163/380 (42.9%) dogs examined. Physical examination and anamnesis indicated 105 (64.4%) positive asymptomatic dogs. Hematological alterations were observed in 115 (70.5%) infected dogs. No clinical, hematological, or epizootiological variable was found to be significantly associated to the infection. In conclusion, the high prevalence of H. canis infection in local dogs may be because of the peri-urban features of this municipality. Moreover, to the best of our knowledge, this study the first study to report H. canis infection in the State of Bahia.