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A Boundary Element based Discontinuous Deformation Analysis (BE-DDA) method is developed by implementing the improved dual reciprocity boundary element method into the open close iterations based DDA. This newly developed BE-DDA is capable of simulating both the deformation and movement of blocks in a blocky system. Based on geometry updating, it adopts an incremental dynamic formulation taking into consideration initial stresses and dealing with external concentrated and contact forces conveniently. The boundaries of each block in the discrete blocky system are discretized with boundary elements while the domain of each block is divided into internal cells only for the integration of the domain integral of the initial stress term. The contact forces among blocks are treated as concentrated forces and the open-close iterations are applied to ensure the computational accuracy of block interactions. In the current method, an implicit time integration scheme is adopted for numerical stability. Three examples are used to show the effectiveness of the algorithm in simulating block movement, sliding, deformation and interaction of blocks. At last, block toppling and tunnel stability examples are conducted to demonstrate that the BE-DDA is applicable for simulation of blocky systems. Copyright © 2016 John Wiley & Sons, Ltd. [ABSTRACT FROM AUTHOR]