After the realization of Haberlandts’ theory of totipotency (Krikorian and Berquam 1969 English translation), in vitro culture of plants has become an integral part of advances in plant science research. Plant tissue culture techniques allow for close monitoring and precise manipulation of plant growth and development, the presence of a controlled environment in vitro to analyze specific source(s) of variation and the possibility of manipulating growth at the cell, tissue and organ levels. These benefits, and others, have given tissue culture and its application paramount importance. It is now possible to understand plant growth and its underlying phenomena in vitro. Aspects of plant growth that were barely understood before the advancement of the science of tissue culture, such as the metabolism and interaction of plant hormones, as well as their physiological effects are now well documented. In addition to its role in the advancement of plant science research, plant tissue culture is also contributing enormously in food production, crop improvement, production of secondary products and conservation of endangered species. The development of tissue culture protocols is a rigorous procedure that involves optimizing the various chemical, physical and environmental factors of growth. It involves growing plants outside their natural environment and growth conditions. The artificial growth conditions are by no means the perfect substitutes for the natural ones. Furthermore, the natural variation in physiology and growth requirement among plant species warrants the need to optimize protocols for individual species. Despite the meticulous efforts involved in growing plants in vitro and the advances made in plant tissue culture, the application of this technique is still hampered by various physiological and developmental problems. The problems range from abnormal growth to increased genetic variability/instability. Papers in this Special Issue report on micropropagation problems related to developmental and physiological aspects such as shoot-tip necrosis (Bairu et al. 2011a), fasciation (Iliev and Kitin 2011), tissue proliferation (Brand 2011), epigenetic changes (Smulders and De Klerk 2011), somaclonal variation (Bairu et al. 2011b), effect of phenolics on rooting (De Klerk et al. 2011), alleviating problems related to caulogenic and rhizogenic processes (Moyo et al. 2011) and assessment of the role of metatopolins in micropropagation and the control of culture abnormalities (Amoo et al. 2011).