Increasing human-animal proximity has also increased risks of zoonotic disease transmission. This study measured the prevalence of anti-Toxoplasma gondii, anti-Leishmania spp. and anti-Leptospira spp. IgG antibodies in dogs and cats attended by the Birth Control Project (BCP) from 2004 to 2012 to determine which environmental variables were significantly associated with infectious agents in the study population. Blood samples from 271 dogs and 415 cats were collected by jugular or cephalic venipuncture for serological analysis. Indirect immunofluorescence assays were used to detect anti-T. gondii and anti-Leishmania spp. IgG antibodies and microscopic serum-agglutination tests were used to detect anti-Leptospira spp. antibodies. Data tabulation and statistical analyses were performed using EpiInfo (3.4.3). Among canine sera samples, 20.6% (56/271), 1.3% (3/236), and 21.6% (51/236) were positive for T. gondii, Leishmania spp., and Leptospira spp., respectively. Higher T. gondii prevalence was found in dogs of unknown breeding history (p=0.0009), those fed raw or undercooked meat (p=0.0101), and those that did not receive the polyvalent vaccine (p=0.0147). There was no statistically significant association between leishmaniosis and leptospirosis and variables evaluated in the epidemiological questionnaire. Among feline sera samples, 20.9% (87/415) were positive for T. gondii. The highest prevalence rates were observed in felines that hunted rodents (p=0.0388) and that consumed untreated water (p=0.0294). These results confirmed that ingestion of raw or undercooked meat, drinking untreated water, and predation of rodents were important risk factors for T. gondii infection. A low Leishmania spp. serodiagnostic prevalence was observed. The most frequent Leptospira spp. serovars were Copenhageni, Canicola, and Butembo.