The yeast comet assay is a fast, sensitive, and inexpensive technique to measure oxidative DNA damage, DNA damage repair, and the genotoxic or protective effects of chemicals. The main advantage over the comet assay using cells of higher organisms is the genetic tractability and ease of cultivation of yeast. A drawback is the lower DNA content of the cells as well as the need for cell wall digestion prior to electrophoresis. Here, we describe in detail a recently developed protocol that permits sensitive and reproducible measurement of DNA damage and DNA repair using Saccharomyces cerevisiae as model system. The combination of this assay with yeast mutants affected in genome maintenance and the wide selection of available yeast molecular biology tools can contribute to illuminate fundamental mechanisms of DNA damage, repair, and activity of DNA protective compounds.