By means of computer-based image analysis it was possible to accelerate and automate a number of originally time-consuming activities in plant pathology and forest protection. In 1997–2005, image analysis was applied to the measuring of the size of colonies of fungi in vitro, feeding mark area, mass measuring of the size of spores and other microscopic objects, assessment of the progress of rot in a stem etc. The paper brings particular examples of the application of image analysis including methodical procedures and examples of research results obtained using Lucia G and Quick Photo Micro programs.