In humans, the study of linear growth at the level of growth plate is limited to the use of mainly noninvasive methods. The use of in vitro studies and diverse animal models are alternative applied methods to unravel the underlying mechanisms of endochondral ossification and bone remodeling. In this chapter, we will outline important techniques to study molecular interactions and the regulation of gene expression in chondrocytes as well as bone cells. Microdissection of growth plate provides a powerful approach to study gene expression of individual zones and temporal senescence of growth plate cartilage by using microarray and real-time PCR analysis. IHC gives valuable information about the distribution of proteins of interest throughout distinct layers of the growth plate. The TUNEL assay has been successfully applied to study apoptosis in chondrocytes. In addition, organ(metatarsal) culture, primary and cell line cultures have been widely used to explore the regulation of chondrocyte differentiation under varying experimental conditions. Ultimately, these methods are essential to give new insights into the search for new diagnostic and therapeutic approaches for growth and various metabolic bone disorders.