We aimed to establish HIV prevalence and uptake of unlinked anonymous testing and voluntary counselling and testing (VCT) among tuberculosis (TB) patients in Jogjakarta, Indonesia. We introduced unlinked anonymous HIV testing for TB patients attending directly observed treatment, short-course services between April and December 2006. Patients were additionally offered VCT services. Of 1269 TB patients who were offered unlinked anonymous testing, 989 (77.9%; 95% CI 75.6-80.1%) accepted. HIV prevalence was 1.9% (95% CI 1.6-2.2%). HIV infections were less frequently diagnosed among TB patients who attended a public health centre [odds ratio (OR) 0.15; 95% CI 0.03-0.70] rather than public hospital. They were more frequent in TB patients with a university education background (OR 5.16; 95% CI 1.01-26.63) or a history of HIV testing (OR 57.87; 95% CI 9.42-355.62). Of the 989 patients who accepted unlinked anonymous testing, only 133 (13.4%; 95% CI 11.5-15.7%) expressed interest in VCT. Of these, 52 (39.1%; 95% CI 31.2-47.6%) attended VCT, but interest was higher among students and those offered VCT by public health centres. The HIV prevalence in Jogjakarta is higher than expected and needs to be monitored cautiously. Unlinked anonymous HIV testing is well accepted and can be implemented with modest additional efforts.