Dogs can be infected by Toxoplasma gondii and Neospora caninum, for which they function, respectively, as intermediate, and definitive hosts. In the present study seroprevalence against T. gondii and N. caninum antibodies, were determined by indirect fluorescent antibody test (cut off of 16 and 50, respectively), in dogs that were treated at public veterinary hospitals in the metropolitan region of São Paulo and risk factors were identified. Out of the 1,194 samples 125 (10.5%; 95% CI: 8.8-12.3%) were positive for T. gondii and 9 (0.75%, 95% CI: 0.34-1.4%) for N. caninum. For T. gondii, statistical differences were observed between the proportions of positive dogs and different zones of the municipality (p = 0.025), and age (p = 0.02), higher among older dogs. The keepers were invited to answer an epidemiological questionnaire to analyze risk factors, and 471 (39.4%) agreed to be interviewed, and among their dogs 65 (13.8%) were T. gondii seropositive. Age group above 8 years (OR = 3.63; 95% CI: 1.08-12.23) was a risk factor and having a defined breed (OR = 0.49; 95% CI: 0.25-0.96) was a protective factor for T. gondii infection. Because of the low number of dogs positive for N. caninum, risk factors for this coccidium were not determined.