A method for correcting erroneous intensity measurements caused by defective pixels of the detector for a single-crystal X-ray diffraction system uses collected diffraction images and a defective pixel list to modify three-dimensional reflection profiles by replacing profile elements affected by the defective pixels with corresponding profile elements from a model profile. Reflection positions on the detector are predicted using an orientation matrix for the crystal and a three-dimensional observed profile is constructed for each reflection. A model profile is constructed using normalized profile data from multiple reflection profiles. The observed profiles are compared with the defective pixel list to determine which profile elements are affected by defective pixels, and those elements are replaced by corresponding elements from the model profile. If the replaced elements represent more than a predetermined percentage of the overall reflection intensity, the data for that reflection is omitted from an overall dataset for the crystal.