We studied patient outcomes by type of referral site following 2 years of combination antiretroviral therapy (cART) during scale-up from June 2006 to July 2011 in Mozambique's rural Zambézia Province. Loss to follow-up (LTFU) was defined as no contact within 60 days after scheduled medication pickup. Endpoints included LTFU, mortality, and combined mortality/LTFU; we used Kaplan-Meier and cumulative incidence estimates. The referral site was the source of HIV testing. We modeled 2-year outcomes using Cox regression stratified by district, adjusting for sociodemographics and health status. Of 7,615 HIV-infected patients ≥15 years starting cART, 61% were female and the median age was 30 years. Two-year LTFU was 38.1% (95% CI: 36.9-39.3%) and mortality was 14.2% (95% CI 13.2-15.2%). Patients arrived from voluntary counseling and testing (VCT) sites (51%), general outpatient clinics (21%), antenatal care (8%), inpatient care (3%), HIV/tuberculosis/laboratory facilities (<4%), or other sources of referral (14%). Compared with VCT, patients referred from inpatient, tuberculosis, or antenatal care had higher hazards of LTFU. Adjusted hazard ratios (AHR; 95% CI) for 2-year mortality by referral site (VCT as referent) were inpatient 1.87 (1.36-2.58), outpatient 1.44 (1.11-1.85), and antenatal care 0.69 (0.43-1.11) and for mortality/LTFU were inpatient 1.60 (1.34-1.91), outpatient 1.17 (1.02-1.33), tuberculosis care 1.38 (1.08-1.75), and antenatal care 1.24 (1.06-1.44). That source of referral was associated with mortality/LTFU after adjusting for patient characteristics at cART initiation suggests that (1) additional unmeasured factors are influential, and (2) retention programs may benefit from targeting patient populations based on source of referral with focused counseling and/or social support.