Objectives This study investigates vitamin D deficiency patterns in individuals from birth to the beginning of adolescence. Microscopic computed tomography (micro‐CT) evaluation of interglobular dentine (IGD) in teeth provides information on the age of disease onset and the number of deficient periods per individual, which will increase our understanding of factors influencing vitamin D deficiency prevalence, including sociocultural practices and latitude. Materials and methods Beemster and Hattem, two Dutch 17th–19th century communities, yielded relatively high prevalences of rickets (15–24%) and residual rickets (15–24%). From the affected individuals, a subsample of 20 teeth were selected for micro‐CT scanning. Thin sections were made of 17 teeth, consisting of 6 teeth with and 11 teeth without observable IGD on micro‐CT that were included for method comparison. Results About 19 out of 29 (65.5%) individuals (one tooth was deemed unobservable) presented with IGD on micro‐CT. Eight of the 11 (72.7%) individuals without IGD on micro‐CT demonstrated histologically visible IGD. In 40.7% (11/27) of the affected individuals (combined micro‐CT and histology results), vitamin D deficiency was recurrent, and in four individuals, some episodes occurred at approximately annual intervals suggesting vitamin D deficiency was seasonal. In three individuals, IGD occurred in the dentine formed around birth, suggesting maternal vitamin D deficiency. Discussion Micro‐CT analysis of IGD is found to be a valuable non‐destructive method that can improve our understanding of the influence of sociocultural practices and latitude on disease development within age and sex groups in past communities.