Growth plates are spatially polarized and structured into three histologically and functionally distinct layers—the resting zone (RZ), proliferative zone (PZ), and hypertrophic zone (HZ). With age, growth plates undergo functional and structural senescent changes including declines of growth rate, proliferation rate, growth plate height and cell number. To explore the mechanisms responsible for spatially-associated differentiation and temporally-associated senescence of growth plate in an unbiased manner, we used microdissection to collect individual growth plate zones from proximal tibiae of 1-week rats and the PZ and early hypertrophic zones of growth plates from 3-, 6-, 9-, and 12-week rats and analyzed gene expression using microarray. We then used bioinformatic approaches to identify significant changes in biological functions, molecular pathways, transcription factors and also to identify specific gene products that can be used as molecular markers for individual zones or for temporal development.