Many of historical structures have degenerated in time by environmental effects, earthquakes, and winds because of the inadequate preservation. The preservation of historical heritage is considered a fundamental issue in the cultural life of modern societies. The protective measures can be supplied if the actual behaviour of the structures is known. The paper presents the results of ambient vibration test and operational modal analysis carried out on the historical masonry bell-tower of the Hagia Sophia church in Trabzon, Turkey. The bell-tower is about 23 m high and dates back to the XIII century. The study includes also the initial analytical model of the tower constituted by the geometrical survey. The experimental measurements are performed using two measurement setups in different times. In the first setup twelve uniaxial accelerometers are used, while in the second setup four triaxial accelerometers with one uniaxial reference are used with the aim of determining the bending and torsional mode shapes as well as natural frequencies and modal damping ratios of the tower. The analytical model of the tower is developed by using solid brick elements, and a relatively large number of finite elements have been used in the model to obtain a regular distribution of mass. The first five natural frequencies and corresponding mode shapes are determined from both theoretical and experimental modal analyses and compared with each other. A good harmony is attained between mode shapes, but there are some differences between natural frequencies. The sources of the differences are introduced in terms of variations in the elasticity modulus of walls, cracks on upper walls, and boundary conditions on base level.