Canine ehrlichiosis and babesiosis have a worldwide distribution with geographic variation in prevalence and main clinical manifestations. We prospectively determined seroprevalence of canine babesiosis and ehrlichiosis, and risk factors for seropositivity. Three hundred and eighty-one dogs were randomly selected to represent the canine population at a Veterinary Teaching Hospital in south Brazil (latitude 23 degrees S). Dogs were tested with a point-of-care ELISA for Ehrlichia canis antibodies and IFA to confirm previous exposure to Babesia vogeli. Multiple logistic regression analysis was then used to estimate adjusted odds ratio (OR) and their 95% confidence intervals. One hundred and thirty-six (36%) dogs were seropositive for B. vogeli antibodies, whereas 87 (23%) dogs were seropositive to E. canis antibodies. Fifty-four (14%) dogs seroreacted to both agents. Adult dogs previously infested with ticks were more likely to seroreact to B. vogeli or E. canis. Superficial bleeding (OR = 12.4) was more common in dogs exposed to B. vogeli, whereas neurological signs (OR = 7.7) were more common in dogs seropositive to E. canis. Neurological signs (OR = 12.0) and lameness (OR = 12.8) were more prevalent in dogs that seroreacted to both organisms. Owners of dogs with ticks were more likely to have been exposed to ticks themselves (OR = 3.2). Canine babesiosis and ehrlichiosis appear to be highly prevalent in this hospital population. Clinical signs differed from the most common signs in other regions with bleeding occurring more in dogs seropositive to babesiosis, but not ehrlichiosis; neurologic signs in dogs with E. canis antibodies; and lameness in dogs that seroreacted to both organisms.