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Background: Despite recent changes to expand the ART eligibility criteria in sub-Saharan Africa, many patients still initiate ART in the advanced stages of HIV infection, which contributes to increased early mortality rates, poor patient outcomes, and onward transmission. Methods: To evaluate individual and clinic-level factors associated with late ART initiation in Mozambique, we conducted a retrospective sex-specific analysis of data from 36,411 adult patients who started ART between January 2005 and June 2009 at 25 HIV clinics in Mozambique. Late ART initiation was defined as CD4 count,100 cells/μL or WHO stage IV. Mixed effects models were used to identify patient- and clinic-level factors associated with late ART initiation. Results: The proportion of patients initiating ART late decreased from 46% to 37% during 2005-2007, but remained constant (between 37-33%) from 2007-2009. Of those who initiated ART late (median CD4 = 57 cells/mL), 5% were known to have died and 54% were lost to clinic within 6 months of ART initiation (compared with 2% and 47% among other patients starting ART [median CD4 = 192 cells/mL]). In multivariate analysis, female sex and pregnancy at ART initiation (AORfemale•not•pregnant•vs.•male = 0.66, 95%CI [0.62-0.69]; AORpregnant•vs.•non•pregnant = 0.60, 95%CI [0.49-0.73]), younger and older age (AOR15-25•vs.26-30 = 0.86, 95%CI [0.79-0.94], AOR.45•vs.26-30 = 0.72, 95%CI [0.67-0.77]), entry into care via PMTCT (AORentry•through•PMTCT•vs.VCT = 0.42, 95%CI [0.35-0.50]), marital status (AORmarried/in union•vs.single = 0.87, 95%CI [0.83-0.92]), education (AORsecondary•or•higher•vs.primary = 0.87, 95%CI [0.83-0.93]) and year of ART initiation were associated with a lower likelihood of late ART initiation. Clinic-level factors independently associated with a lower likelihood of late ART initiation included CD4 machine on-site (AORCD4•machine•onsite•vs.offsite = 0.83, 95%CI [0.74-0.94]) and presence of PMTCT services onsite (AOR = 0.85, 95%CI [0.77-0.93]). Conclusion:: The risk of starting ART late remained persistently high. Efforts are needed to ensure identification and enrollment of patients at earlier stages of HIV disease. Individual and clinic level factors identified may provide clues for upstream structural interventions. [ABSTRACT FROM AUTHOR]