Confocal laser endomicroscopy (CLE) is a promising technology that provides real-time histological visualization of living tissue, described as "optical biopsy". It has been used successfully in dermatology, gastroenterology and ophthalmology for clinical diagnosis and tumor margin assessment. In addition to in vivo tissue assessment, confocal microscopy can also be used ex vivo on freshly excised or fixed tissue for intraoperative tumor margin assessment. While CLE and ex vivo confocal microscopy (EVCM) have shown promising results for the identification of head and neck cancers at cell level, several methodological issues need to be addressed before they can be widely used in routine clinical use. The present review will focus on recent advances in CLE and EVCM in the diagnosis and management of head and neck cancer and discuss remaining challenges for their clinical application.