Age >45 years AHR = 3.33, 95%CI = 1.33–8.31), WHO stage IV (AHR = 3.63, 95%CI = 1.72–7.67), CD4 count <100 cells/mm3 (AHR = 3.79, 95%CI = 1.61–8.91), TB co-morbidity (AHR = 3.39 95%CI = 1.91–6.01) and poor adherence level (AHR = 3.63, 95% CI = 1.89–6.96) at the start of second line ART were significantly associated with second-line ART failure. The gene discussed is CD4; the disease is tuberculosis.