Historical masonry stone mosques with timber truss roofs were widely constructed all over the world. Due to the complex structural behaviors of this type of building, it is difficult to determine natural frequencies during the seismic safety evaluations numerically. The article aims to develop simplified natural frequency formulas based on ambient vibrations for the historical masonry stone mosques with timber truss roofs. Fourteen masonry stone mosques with timber truss roofs built in the Eastern Black Sea Region of Turkey are selected for the study. Experimental natural frequencies, mode shapes and damping ratios of the selected mosques under ambient vibrations are determined using the Operational Modal Analyses. Ambient vibration-based simplified natural frequency formulas based on the geometrical dimensions for the masonry stone mosques with timber truss roofs are obtained by using the statistical regression analysis. The proposed formulas for the first three frequencies are verified with the control data.