Recent advances in computer image analysis techniques allow more accurate quantification of kidney pathological lesions, which are identified by histological staining or immunohistochemistry. This article provides a detailed description of the basic techniques for quantifying these lesions in digital images of light microscopy using Image J software, which is freely available over the Internet. The methods discussed include calibrating measurements, applying scales to images, assessment of object size and thickness, cell counting and point counting, and analysis of area stained. Our explanations indicate how these methods can be used to evaluate glomerular hypertrophy, tubular and vascular injury, accumulation of inflammatory cells and myofibroblasts, deposition of extracellular matrix, and the development of renal scarring.