The primary school children in grades five and eight and secondary school grade two will log everything they eat and drink over the internet.
The survey will also include data on lifestyle, socioeconomic factors as well as blood and urine samples.
The authority hopes the results will provide a picture of the safety and nutritious value of young people’s diets in Sweden and help inform its future policy.
The survey – which will be carried out in full between 2016 and 2017 – follows a smaller pilot study of 300 children recruited through schools last autumn.