Patients undergoing cardiac surgery remain on mechanical ventilation postoperatively until they regain consciousness. Positive end-expiratory pressure (PEEP) may influence the duration of mechanical ventilation after coronary artery bypass grafting (CABG). The aim of this study was to compare the effects of different levels of PEEP on the duration of mechanical ventilation after coronary artery bypass grafting. This was a randomized clinical trial with 136 patients undergoing CABG between January 2011 and March 2012. We divided the patients into three groups with different levels of PEEP at the onset of mechanical ventilation: Group A, PEEP = 5 cmH₂O (n = 44); Group B, PEEP = 8 cmH₂O (n = 47) and Group C, PEEP = 10 cmH₂O (n = 45). Mechanical ventilation time was obtained from a Physical Therapy Evaluation Form. We excluded patients with chronic obstructive pulmonary disease and those requiring concomitant, emergency or off-pump surgeries. For statistical analysis, we used the Kruskal-Wallis, G and Chi-square tests, with p <0.05 considered significant. From the point of weaning from mechanical ventilation until 12 hours after intensive care unit (ICU) admission, we saw a statistically different duration of mechanical ventilation between groups (p = 0.029). In Group A, the average mechanical ventilation time was 6.7 ± 3.2 hours; it was 6.8 ± 3.3 hours in Group B and 5.1 ± 2.9 hours in Group C. The use of higher levels of PEEP was associated with shorter duration of mechanical ventilation in postoperative CABG patients.