This paper presents the results of the first large‐scale study of children from early modern northern Estonia. A total of 191 non‐adults (<17 years) from the 16th–18th century Tõnismägi cemetery in the suburbs of Tallinn were analyzed to gain a better understanding of the health and living environment of these low‐status children. This was achieved through growth analysis and palaeopathological investigation of metabolic and respiratory diseases such as scurvy, vitamin D deficiency, and tuberculosis. Growth disruption was shown to be the most severe among non‐adults aged between 4 and 9 years and comparable to children living in post‐medieval London. It is unlikely that the children from Tallinn would have experienced the same level of industrial hazards as those in London, but poor socioeconomic status, an impoverished diet, and unsanitary living conditions in the suburbs had a detrimental effect on the growth of these non‐adults. This was supported by a statistically significant correlation between growth faltering and respiratory infections and evidence for scurvy in 40% of the infants (n = 30). The most likely cause was early weaning and a diet devoid of vitamin C, induced by poverty and cultural practices. The prevalence of rickets was much lower when compared with other post‐medieval populations in Europe, at just 1.2%. This suggests that children living in Tallinn were not deprived of sunlight and may have had access to more green spaces.