Thidiazuron (TDZ) is a proven effective and potent synthetic plant growth regulator for organogenic, regeneration, and developmental pathways, including axillary and adventitious shoot proliferation, somatic embryogenesis, and in vitro flowering. TDZ has facilitated the establishment of in vitro cultures for several plant species, especially woody and recalcitrant plants, which has enabled their genetic transformation and improvement. Despite the effectiveness and advantages of using TDZ, several drawbacks are associated with its application in plant tissue culture. This review addresses the morphological, physiological, and cytogenetic abnormalities associated with the use of TDZ in vitro, and provides a summary of these abnormalities in several plant species.