Several authors have pointed out the need to identify the optimum operating conditions (OCs) of autothermal thermophilic aerobic digestion (ATAD). This study proves the hypothesis that the OCs have the potential to substantially improve the energy efficiency and plant capacity of established ATAD systems. As ATAD is a semi-batch process, its energy efficiency has to be optimized via dynamic optimization (DO). This methodology requires an adequate mathematical model, and appropriate selection of optimization variables. The paper presents an improved mathematical ATAD model based on previous models found in the literature. A global sensitivity analysis (GSA) was performed in order to identify variables with significant influence upon energy efficiency and plant capacity, thus paving the way for the DO of ATAD systems. The results of the GSA show that reactor volume, reactor temperature, and aeration flowrate are significant variables, which is consistent with reported literature. The results of the GSA also show that both energy efficiency and plant capacity of ATAD systems can be substantially improved by altering reactor volume and OCs. (C) 2009 Elsevier Ltd. All rights reserved.