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In this paper we propose diffusion distance, a new dissimilarity measure between histogram-based descriptors. We define the difference between two histograms to be a temperature field. We then study the relationship between histogram similarity and a diffusion process, showing how diffusion handles deformation as well as quantization effects. As a result, the diffusion distance is derived as the sum of dissimilarities over scales. Being a cross-bin histogram distance, the diffusion distance is robust to deformation, lighting change and noise in histogram-based local descriptors. In addition, it enjoys linear computational complexity which significantly improves previously proposed cross-bin distances with quadratic complexity or higher. We tested the proposed approach on both shape recognition and interest point matching tasks using several multi-dimensional histogram-based descriptors including shape context, SIFT, and spin images. In all experiments, the diffusion distance performs excellently in both accuracy and efficiency in comparison with other state-of-the-art distance measures. In particular, it performs as accurately as the Earth Mover’s Distance with much greater efficiency.