Background: Extra-pulmonary tuberculosis (EPTB) represents about 14% of all cases of tuberculosis (TB) in Malaysia. The aims of the study include evaluation of socio-demographic factors, clinical manifestations, co-morbidities among patients with EPTB and their treatment outcomes.

Methods: A retrospective study was conducted to recognize the epidemiology facts of EPTB. Individual data for EPTB patients were collected from TB registers, laboratory TB registers, treatment cards and TB medical personal files into a standardized study questionnaire. Crude (COR) and adjusted odds ratios (AOR) and 95% confidence intervals (CI) were determined to assess the risk factors for EPTB and unsuccessful treatment outcomes.

Results: There were 1222 EPTB patients presenting 13.1% of all TB cases during 2006–2008. Pleural effusion and lymph node TB were the most frequent types and accounted for 45.1% of all EPTB cases among study participants. Treatment success rate was 67.6%. The best treatment completion rates were found in children ≤15 years (0.478 [0.231–1.028]; p = 0.05). On multivariate analysis, age group 56–65 years (1.658 [1.157–2.376]; p = 0.006), relapse cases (7.078 [1.585–31.613]; p = 0.010), EPTB-DM (1.773 [1.165–2.698]; p = 0.008), patients with no formal (2.266 [1.254–4.095]; p = 0.001) and secondary level of education (1.889 [1.085–3.288]; p = 0.025) were recorded as statistically positive significant risk factors for unsuccessful treatment outcomes. Patients at the risk of EPTB were more likely to be females (1.524 [1.311–1.746]; p < 0.001), Malays (1.251 [1.056–1.482]; p = 0.010) and Indians (1.450 [1.142–1.842]; p = 0.002), TB-HIV (3.215 [2.347–4.405]; p < 0.001), EPDM-HIV (4.361 [1.657–11.474]; p = 0.003), EPTBHIV-HEP (4.083 [2.785–5.987]; p < 0.001), those living in urban areas (1.272 [1.109–1.459]; p = 0.001) and no formal education (1.361 [1.018–1.820]; p = 0.037).

Conclusion: The findings of this study extend the knowledge of EPTB epidemiology and highlight the need for improved EPTB detection in Malaysia, especially in subpopulations with high risk for EPTB and unsuccessful treatment outcomes.