This paper presents evidence for hypomineralization disorders (rickets and osteomalacia) in non-adults at Man Bac, a Neolithic site from northern Vietnam dated to 4000–3500BP, contributing to the well-described disease burden at the site that includes scurvy, treponemal disease, thalassemia, and malaria. Forty-four non-adults (<20 years of age-at-death) were assessed for macroscopic and radiographic evidence for hypomineralization disorders. Differential diagnosis was completed using traditional methods and three-level standardized criteria to combat the challenges of overlapping pathological features between hypomineralization disorder and the other diseases already diagnosed at the site. In addition, a diagnostic certainty approach was applied to investigate the impact of lesion ambiguity on our findings. Kaplan–Meier and Fishers exact tests were applied to assess age-at-death-related epidemiological patterns of hypomineralization disorder and co-morbid relationships with scurvy, thalassemia, and treponemal disease. Almost 50% of the non-adult assemblage presented with evidence for hypomineralization disorder, which was associated with decreased survivorship in childhood. Potential epidemiological relationships between scurvy and hypomineralization disorders, and thalassemia and hypomineralization disorders are described. The former relationship may be due to the likelihood of the introduction of rice resulting in multi-micronutrient deficiency, including vitamin C and calcium deficiency, and cultural attitudes to sunlight. The latter relationship may relate to the pathophysiology of thalassemia that can result in secondary osteomalacia possibly contributing to the development of hypomineralization disorder in the thalassemic non-adults. The findings are significant as they present possible approaches for diagnosis of disease embedded within complex disease burdens where individuals are likely suffering from co-morbidities.