- Tuberculosis (TB) patients who are co-infected with HIV are at greater risk of mortality. Nevertheless, not all countries achieved sustainable and TB and HIV collaboration to describe the burden of both diseases at a national scale. This study aims to describe HIV prevalence among TB-patients in Israel and identify variable associated with TB/HIV co-infection. This retrospective study was conducted by cross-matching the National HIV and TB Registries to describe TB/HIV epidemiology during the last 13-years and define variables predicting TB/HIV co-infection. Between 1999 and 2011, 5,502 TB-patients were reported: 779 (14.2%) were Israeli-born and 4,723 (85.8%) non-Israeli born. Of all TB patients, 254 (4.6%) were HIV-infected. The trend of HIV/TB co-infection among non-Israeli born has generally decreased since 2003 (trend analysis p < 0.001). TB/HIV co-infected patients were mostly males, their TB diagnosis had been performed relatively in shorter time following their arrival in Israel, more likely to be in the 35–44 and 25–34 age groups, non-Israeli born (mostly Africa born), more likely to be culture positive, have multi-drug resistant strains, had worse treatment outcomes and more likely to die treatment than HIV-negative tuberculosis patient. In a multivariate analysis, short time after arrival in Israel, older age, being born in Ethiopia, having positive sputum, positive culture and multi-drug resistant TB predicted TB/HIV co-infection. TB/HIV co-infected patients with extra-pulmonary TB had a higher proportion of infection in lymphatic, miliary and abdominal sites than those with extra-pulmonary TB who were HIV-negative. Most TB/HIV co-infected patients were migrants originating in high-burden countries. Despite the moderate 4.6% TB/HIV co-infection rate in Israel, these patients had worse treatment outcomes and higher mortality rates. This study illustrates the importance of integrating TB with HIV in surveillance and treatment components, which should be employed in other countries, as it has a positive impact on disease control.