HealthNuts is a single-centre,multi-wave, population-based longitudinal study designed to assess prevalence, determinants, natural history and burden of allergy (particularly food allergy) in the early years of life. It is novel in the use of serial food challenge measures within its population frame to confirm food allergy. The cohort comprises 5276 children initially recruited at age 12 months from council-run immunization sessions across Melbourne, Australia. As well as parent-completed questionnaires and researcherobserved eczema status, all infants underwent skin-prick testing to egg, peanut, sesame and either cow's milk or shellfish, and those with detectable wheals underwent food challenges to determine clinical allergy. In wave 2, conducted at age 4 years, validated questionnaires collected data on asthma, allergic rhinitis (hay fever), eczema and food allergies. Food challenges were repeated in children previously identified as food allergic to determine resolution. In wave 3, all children (irrespective of food allergy status) were invited for clinical assessment at age 6 years, including lung function, physical measurements, skin-prick testing to foods and aeroallergens and food challenges if food sensitized. Biological specimens (blood, cheek swabs) were collected at each wave for ancillary immunological, genetic and epigenetic studies. Applications to access data and/or samples can be submitted to [firstname.lastname@example.org].