A cross sectional study was carried out between May and November 2011 to investigate the epidemiological situation of bovine tuberculosis (bTB) in the state of São Paulo, Brazil. The state was divided into seven regions. Three hundred farms from each region, with reproductive activity, were randomly chosen and included as primary sample units. A fixed number of bovine females, older than 2 years of age, were randomly selected and tested, using the comparative cervical tuberculin test. An epidemiological questionnaire based survey was conducted in the selected farms. Our results show that in the state of São Paulo, the apparent prevalence of positive farms was 9% (95% confidence interval, 95% CI = 7.8 - 10.5%). The prevalence in the individual regions varied between 3.5% (95% CI = 1.7 - 6.8%) and 13.9% (95% CI = 10.2 - 18.8%). The apparent prevalence of positive animals in the state was 1.3% (95% CI = 0.9 - 1.7%) and varied from 0.3% (95% CI = 0.2 - 0.6%) to 2.5% (95% CI = 1.4 - 4.5%) in the regions. The risk factors associated with tuberculosis in the state were (i) number of adult females in a herd is = 24 (Odds ratio, OR = 1.91, 95% CI = 1.32 - 2.75), (ii) type of farm enterprise (dairy: OR = 2.70, 95% CI = 1.40 - 5.21; mixed: OR = 2.03, 95% CI = 1.08 - 3.82), (iii) milking process (milking parlor: OR = 4.12, 95% CI = 1.46 - 11.64; portable milking machine: OR = 2.94, 95% CI = 1.42 - 6.09), and (iv) pasture sharing (OR = 1.58, 95% CI = 1.07 - 2.33). The state of São Paulo should implement a structured surveillance system to detect and mitigate the disease. Further, an efficient animal health education program, which encourages the farmers to test replacement animals for bTB prior to introduction in their herds and to avoid pasture sharing with farms of unknown sanitary conditions should also be implemented.