Autism Spectrum Disorder (ASD) is a common neurodevelopmental disorder but effective medical treatments for the core symptoms are still lacking. Although novel genetic and pre-clinical approaches are beginning to identify aetiology-based treatment targets there are still considerable challenges in testing them in clinical trials. This includes the need for objective diagnostic, stratification, and outcome measures that are accepted by international regulatory authorities. The EU-AIMS Longitudinal European Autism Project (LEAP) is a multi-centre, multi-disciplinary study to identify biomarkers that will allow stratification of patients into more biologically homogenous subgroups; and that may serve as surrogate endpoints. The European Medicines Agency (EMA) broadly endorsed the proposed population selection criteria and methodologies (cognitive, eye-tracking, EEG, MRI, FMRI, and biochemical biomarkers) for patient stratification (Loth et al., 2015). This panel will present the first results of the analyses of cognitive tasks, activation tasks using functional MRI, neural network architecture using resting-state MRI data and structural MRI data on volumetry, cortical thickness and surface area. The results will be discussed with the classical case-control paradigm, but also from the perspective of approaches for stratification of ASD.