Over the past decade, the capacity of non-phagocytic cells to produce superoxide has been largely documented. As in the case of the well-characterized phagocytic cells context, superoxide formation in non-phagocytic cells depends on the activity of membrane bound NADPH oxidase enzymes. Six mammalian homologues of the classical phagocytic Nox2 enzyme have been described to date, named Nox1, Nox3, Nox4, Nox5, Duox1 and Duox2, which exhibit similar and specific structure and regulation features. Their biological functions are still poorly understood and were initially mostly deduced from their specific tissue expression profiles. However, recent functional data have emerged that suggest the involvement of several of these isoforms in the innate host response to invading microorganisms, including innate immune and proinflammatory responses. Nox2 is well characterized as a key player in the bacterial killing process that takes place in phagocytes. Here, we will discuss the recent advances that revealed alternative roles of Nox1, Nox4, Duox1 and Duox2 isoforms in other aspects of the innate host defense. In particular, we will focus on their implication in the signaling following pathogen recognition by toll like receptors and in the modulation of dendritic cell functions, two key aspects of innate immunity. Moreover, the potential role of Nox/Duox enzymes in the innate response to virus infections will be discussed.