Air conditioning and cooling systems are one of the most pollutant of the environment in the world and especially our country, because of its warm and dry climate. In this regard, passive systems have an effective role in providing comfort and health of inhabitants. Furthermore they decrease energy consumption. The purpose of this research is to determine the most efficient systems of passive cooling for the desert cities. Isfahan and Yazd has been chosen as case studies. So the efficiency of passive cooling systems has been compared and analyzed in these two cities. The main strategy of this research is descriptive- analytical. To obtain the efficiency of systems, the comfort condition of building has been analyzed before and after using these systems. Afterward the most efficient system has been determined for each city based on the completed analysis of each passive cooling system. The results show that indirect evaporative cooling is the most efficient system in the warmest months of the year for hot and dry climate (B). Night purge ventilation is an efficient system for Isfahan and the cities with the same climate (Bsk) and direct evaporative cooling is an efficient system for Yazd and other cities with the same climate (Bwh).