During the process of tumorigenesis, certain cancers are known to develop deficiencies in one or more major pathways of DNA damage repair, rendering them critically dependent on alternative repair processes for maintaining genomic integrity and viability. Targeting these alternative DNA repair mechanisms is a potentially highly-specific anti-cancer strategy, as their inhibition is theoretically toxic only to tumor cells and not to normal tissues. We will review here the rationale behind this strategy and provide examples of its application. We will also discuss several as yet unanswered questions surrounding this strategy, including whether human cancers frequently harbor synthetically lethal interactions in DNA repair and, if so, how patients might be identified who would benefit from targeting such interactions.