The general topic of the 2016 workshop Heat kernels, stochastic processes and functional inequalities was the study of linear and non-linear diffusions in geometric environments including smooth manifolds, fractals and graphs, metric spaces and in random environments. The workshop brought together leading researchers from analysis, geometry and probability, and provided an excellent opportunity for interactions between scientists from these areas at different stages of their career. The unifying themes were heat kernel analysis, mass transportation problems and functional inequalities while the program straddled across a great variety of subjects and across the divide that exists between discrete and continuous mathematics. Other unifying concepts such as the notions of metric measure space, Otto Calculus and Lott-Sturm-Villani synthetic Ricci curvature bounds played an important part in the discussions. Novel directions including the study of Liouville quantum gravity were included. The workshop provided participants with an opportunity to discuss how these ideas and techniques can be used to approach problems regarding optimal transport, Riemannian and sub-Riemannian geometry, and analysis and stochastic processes in random media.