The increasing prevalence of allergic and auto-immune diseases (AID) has been associated with changes in affluence, life-style and diet. The origins of these non-communicable diseases predominantly occur in early life. While studies have linked allergy and AID prevalence with low intakes of omega-3 Poly-Unsaturated Fatty Acids, vitamins D and E, Zinc and Selenium during the early life, supplementation trials have mostly failed to produce significant benefits. Food allergen avoidance in pregnancy has no effect on allergy risk but potentially adversely effects mother and foetus. The infant gut microbiome has immune regulatory effects but is compromised by a poor diet in pregnancy, and milk formula rather than breast feeding. Pre- and pro- biotics for mother and infant, subtly alters neonatal immune function but rarely clinical outcomes. Nevertheless, there are generic benefits from an over-all healthy diet during pregnancy, with regular exercise, no smoking, antibiotics or Caesarean section delivery. Maternal and infant obesity increases risks of allergy and AID, and weight reduction is indicated. Avoidance of ultra-processed foods is recommended as they increase obesity, cardio-vascular and mental health disorders. Breast feeding, early introduction of common allergenic foods, and a healthy fresh food diet after weaning reduce risks. A multi-faceted approach is most likely to achieve optimal life-long health.