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Little is known about outcomes after transfer out (TFO) and loss to follow-up (LTF) and how differential outcomes might bias mortality estimates, as analyses generally censor or exclude TFOs/LTF. Using data linked to the National Population Register, we explored mortality among TFO and LTF patients compared with patients who were retained and investigated how linkage impacted on mortality estimates.A cohort analysis of routine data on adults with civil identification numbers starting antiretroviral therapy (ART) 2004–2009 in 4 large South African ART cohorts. The number, proportion, timing, and mortality of TFOs and LTF were reported. Mortality was compared using Kaplan–Meier curves, Cox's proportional hazards, and competing risks regression.Before linkage, 1207 patients (6%) had died, 2624 (13%) were LTF, 1067 (5%) were TFO and 14,583 (75%) were retained. Compared with retained, mortality risk was 3 times higher among TFO patients [adjusted hazard ratio (aHR), 3.11; 95% confidence interval (CI): 2.42 to 3.99] and 20 times higher among LTF patients (aHR, 22.03; 95% CI: 20.05 to 24.21). Excluding early deaths after TFO or LTF, the risk was comparable among TFOs and retained (aHR, 0.75; 95% CI: 0.54 to 1.03) and higher among LTF (aHR, 2.85; 95% CI: 2.43 to 3.33). After linkage, corrected mortality was higher than site-reported mortality. Censoring did not, however, lead to substantial underestimation of mortality among TFOs.Although TFO and LTF predicted mortality, the lower incidence of TFO and subsequent death compared with LTF meant that censoring TFOs did not bias mortality estimates. Future cohort analyses should explicitly consider proportions of TFO/LTF and mortality event rates.