In order to optimize the conditions for evaluation of isoelectric focusing (IEF) patterns by digital image processing, the sources of error in determination of the pi values were analyzed together with the influence of a varying background. The effects of band distortions, in the spectra of the individual lanes, were examined. In order to minimize the effect of these distortions, optimal conditions for handling IEF patterns by digital image processing were elucidated. The systematic part of the global deformation on the gels was investigated and an algorithm was developed by which it was possible to correct for a part of the individual distortions. The effects of various corrections for lane distortions were illustrated by classification, using different types of discriminant analysis. Finally the background disturbances were examined, and described by a mathematical model.