Under certain conditions, repetitive DNA motifs have the potential to adopt non-B-form DNA structures, such as hairpins, triplexes, Z-DNA, quadruplexes, and i-motifs. Some non-B-form DNAs have been proposed to cause mutations and, consequently, participate in several biologically important processes, including regulation, evolution, and human disease. Advancement in the knowledge of specific interactions between molecules and non-B-form DNAs at the molecular level in living cells is important for understanding their biological functions. In this review, we describe the latest studies on molecules that target non-B-form DNAs in vivo, with a focus on Z-DNA, G-quadruplexes, triplexes, i-motifs, and hairpins.