A multifactorial approach is taken to observe for changes in childhood health in Medieval and Early Modern Denmark. Samples originate from three cemeteries located in the urban cities of Horsens and Odense. The dates of theses samples are of particular interest due to historic records documenting the Middle Ages as a time of hardship with extreme fluctuations in climate impacting agriculture and food availability as well several repeated waves of deadly plague. Variations in health are observed in the form of longitudinal growth, body size, epiphyseal growth and cortical thickness;​ encompassing various facets of the growth and development processes. Cortical thickness has not been thoroughly applied to studies of health and physiological stress despite evidence of its value. Unlike previous work that has relied on 2D measurements from X-rays, 3D imaging is used to visualize the bone structure and measure appositional growth. There is no evidence of stunted growth or development delay between temporal periods. This could suggest that the documented hardships of the Middle Ages were mitigated by Denmark’s unique environment and marine access, or could be evidence of cultural value and protection of children. There is however, a temporal change in age-related mortality patterns with an increase in individuals aged 14 to 18 in 1250-1450 but low infant mortality. By contrast, in the post-Reformation sample, there is an increase in infant mortality and decrease in older child and adolescent deaths. CT imaging of cortical thickness provided an effective means of studying appositional growth in a past population and observations show potential for greater sensitivity in identifying physiological stress than the traditional use of longitudinal growth.