In this paper, using the governance, resources and processes model for an organization, we examine the organizational challenges for innovation in information systems in each of the three areas of this model. Information systems are a great tool to support innovation to improve the processes and activities in an organization to achieve a competitive edge. We review the role of leadership (governance), intellectual capital (resources) and organizational culture (processes) on incremental and radical innovation in information systems. The existing research suggests that a democratic organizational culture fosters organizational learning and innovation whereas a hierarchical culture acts as a barrier. In information systems, the three phases of innovation include the concept, development and commercialization. The organizational challenges associated with the concept phase of the innovation in the information systems are reviewed. To explore the organizational challenges in the development and commercialization phases in terms of governance, resources and processes, a qualitative research proposal is presented.