Soma-clonal variation comprises genetic or epigenetic changes that arise during the in vitro culture phase of somatic cells (cell, tissue, organ cultures, etc.). In plant breeding programs, soma-clonal variation might become an important source of variability. However, this kind of variation is undesirable for micro-propagation purposes and for germplasm conservation in vitro, where genetic fidelity is desired. Therefore, a series of molecular techniques has been used for detection of soma-clonal variation. This review presents a description of the main molecular techniques used to detect in vitro soma-clonal variation. Moreover, a compilation of scientific papers related to the detection of soma-clonal variation by molecular techniques is presented.