The occurrence of the black rat, Rattus rattus , in major Brazilian cities has increased in the recent years. To evaluate if the efforts of public rodent control have been reaching the species in the city of São Paulo, a survey was conducted in flooding areas using live trapping before and after implementation of the control program. Captures were carried out from 2009 to 2011, and animals were evaluated for their risk of zoonosis transmission. The number of R. rattus captured after control did not differ from the number of animals captured before the control program in the Spring/Summer season, but, in the Autumn/Winter season, effective control was observed. Low infestations of Ctenocephalides felis (Siphonaptera) and Echinolaelaps echidninus (Acarina) were observed, and antibodies against Leptospira spp. were detected in just 1 of 65 serum samples. Ten out of 18 serum samples were sororeactive for Vaccinia virus, suggesting contact between R. rattus and the pathogen Calodium hepaticum (= Capillaria hepaticum ) (Nematoda) was found in the liver of 73.4% of captured R. rattus. In conclusion, R. rattus may not be effectively controlled by the rodent Control Program in the city of São Paulo, and represents a threat to human health, justifying permanent environmental management and educational programs.