Eggs have been shown to be a rich source of several vitamins and minerals and that increased consumption improves growth and prevents stunting in children, however the mechanism behind this is not fully understood. This randomised control trial of 75 children aged 8-14 years aimed to determine the effect of prolonged egg supplementation on insulin-like growth factor 1 (IGF-1), which is involved in bone development and the production of metabolites known as short-chain fatty acids (SCFAs) by gut microbiota. The results showed that consuming 10 additional whole eggs per week in addition to their usual egg consumption for 35 weeks resulted in increased IGF-1 levels compared to control. The production of SCFAs remained the same with whole egg supplementation as with control. The production of IGF-1 was associated with the production of the beneficial SCFAs propionate, butyrate, isovalerate, and valerate. Interestingly however, the consumption of whole eggs also increased the production of some gut microbiota associated metabolites, which have been shown to have adverse health effects. It was concluded that increased whole egg consumption may promote bone health and growth in children and that the association between IGF-1 and SCFAs indicates a connection between diet, microbiota, and health. This study could be used by healthcare professionals to consider the recommendation of increased egg consumption in children to promote bone health and growth. It should be noted that the children used in this study were from rural Thailand, where undernourishment may be an issue.