The calculations of fuel tanks should take into account the geometric imperfections of the structure as well as the variability of the material parameters of the foundation. The deformation of the tank shell can have a significant impact on the limit state of the structure and its operating conditions. The paper presents a probabilistic analysis of a vertical-axis, floating-roof cylindrical shell of a tank with a capacity of 50000 m3 placed on stratified soil with heterogeneous material parameters. The impact of a random subsoil description was estimated using the Point Estimated Method (PEM). In this way, the number of analyzed FEM models was significantly reduced. This approach also makes it possible to assess the sensitivity of tank settlement and deformation to the changing foundation conditions.