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Introduction: Loss-to-follow-up (LTFU) in the prevention of mother-to-child HIV transmission (PMTCT) programmes can occur at multiple stages of antenatal and follow-up care. This paper presents findings from a national assessment aimed at identifying major bottlenecks in Côte d'Ivoire's PMTCT cascade, and to distinguish characteristics of high- and low-performing health facilities., Methods: This cross-sectional study, based on a nationally representative sample of 30 health facilities in Côte d'Ivoire used multiple data sources (registries, patient charts, patient booklets, interviews) to determine the magnitude of LTFU in PMTCT services. A composite measure of retention - based on child prophylaxis, maternal treatment and infant testing - was used to identify high- and low-performing sites and determine significant differences using Student's t-tests., Results: Among 1,741 pregnant women newly recorded as HIV-positive between June 2011 and May 2012, 43% had a CD4 count taken, 77% received appropriate prophylaxis and 70% received prophylaxis intended for their infant. During that time, 1,054 first infant HIV tests were recorded. A conservative rate of adherence to antiretroviral therapy was estimated at 50% (n=219 patient charts). Significant differences between high- and low-performing sites included: duration of time elapsed between HIV testing and CD4 results (29.5 versus 56.3 days, p=0.001); and density (number per 100 first antenatal care visits) of full-time physicians (6.7 versus 1.7, p=0.04), laboratory technicians (2.3 versus 0.7, p=0.046), staff trained in PMTCT (10.7 versus 4.7, p=0.01), and staff performing patient follow-up activities (7.9 versus 2.5, p=0.02). Key informants highlighted staff presence and training, the availability of medical supplies and equipment (i.e., on-site CD4 machine), and the adequacy of infrastructure (i.e., space and ventilation) as perceived key factors positively and negatively impacting retention in care., Conclusions: Patient LTFU occurred throughout the PMTCT cascade from maternal to infant testing, with retention scores ranging from 0.10 to 0.83. Sites that scored higher had more dedicated and trained frontline health workers, and emphasised patient follow-up through outreach and the reduction of delays in care. Strategies to improve patient retention and decrease transmission should emphasise patient tracking systems that utilise critical human resources to both improve data quality and increase direct patient follow-up.