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Abstract Background Severe tooth decay is known to affect the health and well-being of young children. However, little is known about the influence of Severe Early Childhood Caries (S-ECC) on childhood nutritional status. The purpose of this study was to contrast ferritin and haemoglobin levels between preschoolers with S-ECC and caries-free controls. Methods Children were recruited as part of a larger case–control study examining differences in nutritional status between those with and without S-ECC. Preschoolers with S-ECC were recruited on the day of their dental surgery, while caries-free controls were recruited from the community. Parents completed a questionnaire and the child underwent venipuncture. The study was approved by the University’s Health Research Ethics Board. Statistics included descriptive, bivariate and logistic regression analyses. A p value ≤ .05 was significant. A total of 266 children were recruited; 144 with S-ECC and 122 caries-free. Results The mean age was 40.8 ± 14.1 months. The mean ferritin concentration for all children was 29.6 ± 17.9 μg/L while the mean haemoglobin level was 115.1 ± 10.1 g/L. Children with S-ECC were significantly more likely to have low ferritin (p=.033) and low haemoglobin levels (p>.001). Logistic regression analyses revealed that children with S-ECC were nearly twice as likely to have low ferritin levels and were over six times more likely to have iron deficiency anaemia than caries-free controls. Conclusions Children with S-ECC appear to be at significantly greater odds of having low ferritin status compared with caries-free children and also appear to have significantly lower haemoglobin levels than the caries-free control group. Children with S-ECC also appear to be at significantly greater odds for iron deficiency anaemia than cavity-free children.