Retention in anti-retroviral therapy (ART) presents a challenge in sub-Saharan Africa. In Mozambique, after roll-out to peripheral facilities, the 12-month retention rate was reported mostly from sites with an electronic patient tracking system (EPTS), representing only 65% of patients. We conducted a nationally representative study, compared 12-month retention at EPTS and non-EPTS sites, and its predictors. Methods Applying a proportionate to population size sampling strategy, we obtained a nationally representative sample of patients who initiated ART between January 2013 and June 2014. We calculated weighted proportions of the patients’ status at 12 months after ART initiation, and 12-month incidence of lost to follow-up (LTFU) and death. We assessed determinants of LTFU and death by calculating adjusted hazard ratios (AHR) through multivariate cox-proportional hazard models. Results Among 19,297 patients sampled, 54.3% were still active, 33.1% LTFU, 2.0% dead, 2.6% transferred-out and 8.0% had unknown status, 12 months after ART initiation. Total attrition rate (LTFU or dead) was 45.5/100PY, higher at facilities without EPTS (51.8/100PY) than with EPTS (37.7/100PY). Clinical stage IV (AHR = 1.7), CD4 count 150 (AHR = 1.3) and being pregnant (AHR = 1.6) were significantly associated with LTFU. Clinical stage III or IV (AHR = 2.1 and 3.8), CD4 count 150 (AHR = 3.0), not being pregnant (AHR = 3.0), and ART regimens with stavudine (AHR = 4.28) were significantly associated with deaths. Patients enrolled in adherence support groups were 4.6 times less likely to be LTFU, but the number (n = 174) was too small to be significant (p = 0.273)