In step-and-shoot IMRT plans, aperture-based optimization (or one-step optimization) has been considered as a means of improving monitor unit (MU) efficiency compared to fluence-based optimization (or two-step optimization). However, the extent of improvement on MU efficiency varies, depending on the implementation and design of one-step optimization. In this paper, we attempted to investigate MU efficiency issue in two methods of one-step optimization implemented in two commercial treatment planning systems (TPSs). Five patients with nasopharyngeal cancer and five patients with advanced prostate cancer were selected for this study. For these patients, clinically used IMRT plans were generated using the Direct Machine Parameter Optimization (DMPO) in the Pinnacle TPS. New IMRT plans were created using the Direct Aperture Optimization (DAO) method in the Panther TPS. For the purpose of this study, we used the similar planning dose objectives and beam configurations with a similar total number of segments in each pair of DMPO and DAO plans. With similar plan quality, DMPO plans required more MUs than DAO plans. The average number of MUs (expressed in mean ± 1 SD) for the DMPO and DAO plans was 1,169 ± 186 and 671 ± 135 for the nasopharynx cases, and 711 ± 48 and 400 ± 65 for the prostate cases, respectively. The average segment areas (expressed in mean ± 1 SD) for the DMPO plans were smaller than those for the DAO plans: 46.0 ± 7.6 cm2 vs. 100.9 ± 32.3 cm2 for the nasopharynx cases, and 58.3 ± 17.2 cm2 vs. 97.4 ± 35.0 cm2 for the prostate cases, respectively. In conclusion, two one-step optimization algorithms, DMPO and DAO, resulted in much different MU efficiency with the similar number of segments and optimization parameters. This MU difference is largely attributed to the fact that large area segments are used more often in DAO plans than in DMPO plans.