Consumers expect organic products to be healthier. However, limited research has been performed to study the effect of organic food on health. The present study aimed to identify biomarkers of health to enable future studies in human subjects. A feeding experiment was performed in two generations of three groups of chickens differing in immune responsiveness, which were fed identically composed feeds from either organic or conventional produce. The animals of the second generation were exposed to an immune challenge and sacrificed at 13 weeks of age. Feed and ingredients were analysed on macro- and micronutrients, i.e. vitamins, minerals, trace elements, heavy metals and microbes. The chickens were studied by general health and immune parameters, metabolomics, genomics and post-mortem evaluation. The organic and conventional feeds were comparable with respect to metabolisable energy. On average, the conventionally produced feeds had a 10 % higher protein content and some differences in micronutrients were observed. Although animals on both feeds were healthy, differences between the groups were found. The random control group of chickens fed conventional feed showed overall a higher weight gain during life span than the group on organic feed, although feed intake was mostly comparable. The animals on organic feed showed an enhanced immune reactivity, a stronger reaction to the immune challenge as well as a slightly stronger ‘catch-up growth’ after the challenge. Biomarkers for future research were identified in the parameters feed intake, body weight and growth rate, and in immunological, physiological and metabolic parameters, several of these differing most pronounced after the challenge.