Joint genetic and neuroimaging data analysis on large cohorts of subjects is a new approach used to assess and understand the variability that exists between individuals. This approach has remained poorly understood so far and brings forward very significant challenges, as progress in this field can open pioneering directions in biology and medicine. As both neuroimaging – and genetic-domain observations represent a huge amount of variables (of the order of 10^6), performing statistically rigorous analyses on such big data represents a computational challenge. In the A-Brain project, we address this computational problem by using cloud computing techniques on the Microsoft Azure cloud. By using a storage-optimised MapReduce engine, we are able to distribute the analysis among multiple cloud nodes to perform this joint analysis.