The aim of this study was to describe the effect of non-adherence on the main laboratory outcomes, TCD4+ lymphocyte count and viral load, routinely used to monitor patients initiating treatment according to three different approaches to measure adherence to antiretroviral therapy. Among 288 participants, 22.9%, 31.9% and 74.3% were considered non-adherent, according to medical charts, self-report and pharmacy records, respectively. Depending on the adherence measures used, the average gain in TCD4+ lymphocyte count ranged from 142.4 to 195.4 cells/mm3 among adherent patients, and from 58.5 to 99.8 lymphocytes TCD4+/mm3 among those non-adherent. The average reduction on viral load ranged from 4.25 to 4.62 log copies/mL among the adherent patients, and from 1.99 to 4.07 log among those non-adherent. Monitoring antiretroviral adherence should be considered a priority in these public AIDS referral centers in order to identify patients at high risk of developing virologic failure. Early interventions are necessary in order to maintain the initial therapeutic regimens for longer periods.