The particulate discrete element method (DEM) can be employed to capture the response of rock, provided that appropriate bonding models are used to cement the particles to each other. Simulations of laboratory tests are important to establish the extent to which those models can capture realistic rock behaviors. Hitherto the focus in such comparison studies has either been on homogeneous specimens or use of two-dimensional (2D) models. In situ rock formations are often heterogeneous, thus exploring the ability of this type of models to capture heterogeneous material behavior is important to facilitate their use in design analysis. In situ stress states are basically three-dimensional (3D), and therefore it is important to develop 3D models for this purpose. This paper revisits an earlier experimental study on heterogeneous specimens, of which the relative proportions of weaker material (siltstone) and stronger, harder material (sandstone) were varied in a controlled manner. Using a 3D DEM model with the parallel bond model, virtual heterogeneous specimens were created. The overall responses in terms of variations in strength and stiffness with different percentages of weaker material (siltstone) were shown to agree with the experimental observations. There was also a good qualitative agreement in the failure patterns observed in the experiments and the simulations, suggesting that the DEM data enabled analysis of the initiation of localizations and micro fractures in the specimens.