A quaternion formulation is used to derive an algorithm for performing calculations on molecular clusters using the quantum diffusion Monte Carlo method. It is assumed that the monomers in the cluster rotate and translate as rigid bodies. The algorithm is tested on the water dimer and the benzene-water cluster. Comparison with dissociation energies and rotational constants obtained with other methods illustrates the accuracy of the algorithm. (C) 2000 American Institute of Physics. [S0021-9606(00)00635-8].