The Milieu Intérieur (MI) project, coordinated by Institut Pasteur, was established in 2011 with the aim to define the parameters that characterise a healthy immune response and its natural variation across individuals, and in doing so, inform clinical strategies for managing disease. For this, 1000 healthy volunteers (1:1 sex ratio; stratified across 5 decades of life from 20 to 69 years of age) were recruited. For each individual, a detailed eCRF of lifestyle and demographic variables, whole blood for immune phenotyping, immune stimulation and genomic analysis, as well as faecal samples and nasal swabs for metagenomic studies of microbiota, were collected. Punch skin biopsies were also taken to generate primary fibroblast lines and iPSc (from selected donors) to enable mechanistic studies. The MI project has provided a definition of protein and transcriptional immune signatures for healthy immune responses. The project also revealed new insights into the genetic and non-genetic factors driving immune response variation. In addition to key fundamental insights, the MI project has established a rich sample repository and data-warehouse, supporting ongoing integrative research in systems immunology.