An analytical method is proposed to investigate the wave diffraction of linear waves with a uniform, bottom-mounted cylinder with an arbitrary smooth cross-section. Based on the condition that the radius function of the cylinder surface can be expanded into a Fourier series, the linear diffraction theory is extended to solve the diffraction problem of linear waves in such large-scale structures. The present method is first validated using a uniform vertical cylinder with cosine-type radial perturbations. Then, the wave diffraction, wave force and wave run-up are investigated for such structures under wave attacks with different rotation angles. Finally, this method is further extended to a practical engineering appli- cation in a quasi-ellipse caisson foundation for a cross-strait bridge pylon. The results show that the method that we have developed can be effectively used for predicting the wave force and wave run-up of large-scale cylinders with arbitrary smooth cross-sections considering the wave diffraction effects