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Exclusive breastfeeding for the first 6 months is recommended by the World Health Organization and considered allergy preventive. However, it is not known whether prolonging exclusive breastfeeding for over 6 months provides further benefit in allergy prevention.The aim of this prospective 20-year follow-up study was to find out whether the allergy protective effect can be enhanced by prolonging strictly exclusive breastfeeding for ≥9 months of age.A total of 200 unselected healthy newborns were enrolled in the study. Their mothers were encouraged to maintain exclusive breastfeeding for as long as possible. The number of infants on strictly exclusive breastfeeding was 167 at 2, 116 at 6, 36 at 9 and 7 at 12 months of age. Of the 200 infants, 42% had a family history of allergy. The children were re-assessed at ages 5 (n = 163), 11 (n = 150) and 20 years (n = 164) with clinical examination, skin prick testing, and parental and personal structured interviews.Exclusive breastfeeding prolonged for ≥9 months was associated with atopic dermatitis (P = 0.002) and symptoms of food hypersensitivity (P = 0.02) at age 5 years, and with symptoms of food hypersensitivity at age 11 years (P = 0.01), in children with a family history of allergy.Prolonging strictly exclusive breastfeeding for ≥9 months was not helpful in atopy prevention, instead, it was associated with increased atopic dermatitis and food hypersensitivity symptoms in childhood.