BACKGROUND: Tuberculosis is the most common opportunistic infection among HIV-infected patients in Brazil. Brazil's national policy for HIV care recommends screening for latent tuberculosis (TB) and implementing isoniazid preventive therapy (IPT). OBJECTIVES: We compared physician adherence to TB screening and other prevention and care policies among HIV primary care clinics in Rio de Janeiro City. METHODS: Data on performance of CD4 counts, viral load testing, tuberculin skin testing (TST) and IPT were abstracted from patient charts at 29 HIV clinics in Rio de Janeiro as part of the TB/HIV in Rio (THRio) study. Data on use of pneumocystis jiroveci pneumonia (PCP) prophylaxis were also abstracted from a convenience sample of 150 patient charts at 10 HIV clinics. Comparisons were made between rates of adherence to TB guidelines and other HIV care guidelines. RESULTS: Among the subset of 150 patients with confirmed HIV infection in 2003, 96% had at least one reported CD4 counts result; 93% had at least one viral load result reported; and, PCP prophylaxis was prescribed for 97% of patients with CD4 counts < 200 cells/mm³ or when clinically indicated. In contrast, 67 patients (45%) had a TST performed (all eligible); and only 11% (17) of eligible patients started IPT. Among 12,027 THRio cohort participants between 2003 and 2005, the mean number of CD4 counts and viral load counts was 2.5 and 1.9, respectively, per patient per year. In contrast, 49% of 8,703 eligible patients in THRio had a TST ever performed and only 53% of eligible patients started IPT. CONCLUSION: Physicians are substantially more compliant with HIV monitoring and PCP prophylaxis than with TB prophylaxis guidelines. Efforts to improve TB control in HIV patients are badly needed.