Retention in early HIV care has been associated with decreased mortality and improved viral suppression, however the consequences of poor retention in early care in Brazil remain unknown. We assessed the effect of poor retention on mortality in a Brazilian HIV-infected clinical cohort. The analysis included ART-naïve, HIV-infected adults linked to care at the Instituto Nacional de Infectologia Evandro Chagas, Fundação Oswaldo Cruz between 2000 and 2010, who did not become pregnant nor participate in a clinical trial during the first two years in care (early care). Poor retention in early care was defined as less than 3 out of 4 six-month intervals with a CD4 or HIV-1 RNA laboratory result during early care. Cox proportional hazards models were used to identify factors associated with mortality, and Kaplan-Meier plots were used to describe the survival probability for participants with poor retention versus good retention. Among 1054 participants with a median (interquartile range) follow-up time of 4.2 years (2.6, 6.3), 20% had poor retention in early care and 8% died. Poor retention in early care [adjusted hazard ratio (aHR) 3.09; 95% CI 1.65-5.79], AIDS defining illness (aHR 1.95; 95% CI 1.20-3.18) and lower education (aHR 2.33; 95% CI 1.45-3.75) were associated with increased mortality risk. Our findings highlight the importance of adopting strategies to improve retention in early HIV care.