The reflection of regular and irregular waves from a partially perforated caisson breakwater with a rock-filled core is examined. The present mathematical model is developed by means of the matched eigenfunction method. Numerical results of the present model are compared with the experimental data of different researchers. Numerical examples are given to examine the effect of rock fill on the reflection coefficient. The differences between regular and irregular waves are also investigated by means of theoretical and experimental results. It is found that the minimum reflection coefficient of irregular waves is larger than that of corresponding regular waves, but the contrary is the case for the maximum reflection coefficient. The reflection of regular and irregular waves from a partially perforated caisson breakwater with a rock-filled core is examined. The present mathematical model is developed by means of the matched eigenfunction method. Numerical results of the present model are compared with the experimental data of different researchers. Numerical examples are given to examine the effect of rock fill on the reflection coefficient. The differences between regular and irregular waves are also investigated by means of theoretical and experimental results. It is found that the minimum reflection coefficient of irregular waves is larger than that of corresponding regular waves, but the contrary is the case for the maximum reflection coefficient.