We propose the use of anisotropic diffusion filtering to remedy difficulties in analysis of electronic portal images, stemming from their low contrast and high noise levels. Anisotropic diffusion is a nonlinear filter based on the numerical solution to the partial differential equation describing the process of diffusion. In this study we show that this filter is capable of greatly reducing noise in homogeneous areas of portal images while preserving the edges and contrast associated with anatomical features. We also demonstrate that the application of anisotropic diffusion leads to more consistent and reproducible visual extraction of features from portal images.