Mosques are places of worship for Muslims with unique functional requirements and operational characteristics. They are partially or fully occupied for about an hour for five intermittent periods during the day. In hot climates, maintaining indoor thermal comfort requires a considerable amount of energy that can be reduced by proper operational zoning and effective HVAC operation strategies. The objective of this paper is to investigate the impact of operational zoning and HVAC system intermittent operation strategies on the energy performance of mosques while thermal comfort is maintained. Energy simulation modeling is used for evaluating alternative zoning and HVAC operation strategies. Results indicate that up to 23% reduction in annual cooling energy is achieved by employing suitable HVAC operation strategy and system over-sizing, and 30% reduction is achieved by appropriate operational zoning. Comparing the cooling energy consumption of HVAC summer continuous operation of an un-insulated mosque with the consumption of the insulated mosque with properly oversized HVAC system operated for 1 h during each prayer, indicated that as much as 46% of cooling energy reduction can be achieved. Furthermore, utilizing proper operational zoning and HVAC operation strategies is expected to bring about an additional significant energy reduction. Guidelines for mosque HVAC systems operation and thermal zoning are developed. These design/operation guidelines would provide a source of information for professionals to improve the thermal and energy performance of mosques. This knowledge can also contribute towards the development of future energy-related design codes for mosques. (C) 2013 Elsevier Ltd. All rights reserved.