The accurate calculation of run-up heights of long waves along the coastline is important in the view of engineering. In this paper the run-up heights of long waves are estimated by using the cnoidal wave theory which also covers both sinusoidal and solitary waves. However, the generation and the calculation of run-up heights of cnoidal waves are difficult both in laboratory and numerical experiments. In this study, the maximum run-up heights of cnoidal waves on steep slopes are computed by using the boundary integral equation model. It has been shown that the run-up heights of cnoidal waves are less than those of solitary waves, while they are larger than those of sinusoidal waves having the same wavelengths and heights. The variation of run-up heights of cnoidal waves is not a monotonic function of the wavelength. However, the run-up heights of cnoidal waves asymptotically approach that of a solitary wave as the wavelength approaches infinity. The calculated run-up heights agreed reasonably with experimental data.