BACKGROUND: The aim of this study was to identify health-related biomarkers affected by different growth conditions of plant foods. Rats were fed balanced diets composed of vegetables and rapeseed oil from three different cultivation systems ('LIminusP', low fertiliser input, without pesticides; 'LIplusP', low fertiliser input, with pesticides; and 'HIplusP', high fertiliser input, with pesticides) chosen to cover a broad range of management options, rather than representing actual food production systems.