Abstract Regarding clinically-concerning non-standard initial anti-tuberculous (TB) regimens, few studies have examined their prevalence, risk factors and impacts. We recruited patients with drug susceptible TB and non-standard initial anti-TB regimens (NSTB group) and matched them with patients with standard initial regimens (STB group) in a 1:1 ratio. The risk factors and outcomes were analyzed. During the 11-year study period, we analyzed 50 (3.7%) patients with NSTB from a total set of 1337 patients with drug-susceptible TB. Pyrazinamide (60%) was the drug most commonly not prescribed in the NSTB group, followed by ethambutol (34%). Multivariable logistic regression identified independent risk factors as underlying eye disease (adjusted odds ratio [aOR]: 8.869; 95% CI 2.542–30.949; p = 0.001), gout/hyperuricemia (aOR: 4.012 [1.196–13.425]; p = 0.024), and liver disease (aOR: 12.790 [3.981–41.089]; p