This paper provides an overview of the studies that were conducted in our laboratories in the last decade on hetero-atom doped carbon structures as potential oxygen reduction reaction (ORR) catalysts for PEM fuel cells. These studies include evaluating the potential of nitrogen doped carbon nanostructures as cathode catalysts for proton exchange membrane and direct methanol fuel cells and examining the nature of the transition metal used as growth catalysts in synthesis of these materials, through activity and in situ and ex situ characterization experiments. These studies also shed some light on the ongoing debate about the differences and similarities between two classes of materials used for ORR, namely FeNC and CNx catalysts, through activity and stability tests, X-ray absorption spectroscopy, X-ray photoelectron spectroscopy, Mossbauer spectroscopy, temperature-programmed techniques and selective poisoning experiments designed to probe the active sites.