The base excision repair pathway is a critical mechanism that removes non-bulky DNA lesions arising from base oxidation, alkylation, or deamination. Base excision repair is initiated by enzymes called DNA glycosylases that excise the damaged base, and then require additional proteins to remove the sugar–phosphate moiety, fill the subsequent nucleotide gap and perform ligation. Studies on base excision repair mechanisms in plants have been traditionally neglected, in comparison to those performed in bacteria, yeast or mammals. However, significant advances have been made in the last two decades, mainly in the model organism Arabidopsis thaliana but also in other plant species. The results obtained so far indicate that plants have base excision repair proteins similar to those previously identified in other organisms. However, they also possess some plant-specific base excision repair proteins, as well as distinctive combinations of enzymes not found in other kingdoms. Importantly, plant base excision repair has evolved to perform important additional functions, such as erasing of epigenetic marks in DNA.