For a long time, it has been known that optics can provide a broad range of tools for addressing clinical needs, particularly diagnostics. Optical techniques can help in identifying diseases and detecting pathological tissues with non/minimally invasive and label-free methods. Given the current limitations of standard clinical procedures, such an approach could provide a powerful tool in detecting gastrointestinal and bladder cancers. However, each technique has serious limitations regarding one or more of the following features: biomarker sensitivity, penetration depth, acquisition times, or adaptation to the clinical environment. Hence there is an increasing need for approaches and instruments based on the concept of multimodality; in this regard, we review the application of different imaging/spectroscopy tools and methods operating in the first two optical windows (SHG, SPEF, TPEF, THG, 3PEF, CARS, Raman and reflectance) for tumour detection in the digestive and urinary systems. This article also explores the possibility of exploiting the third bio-tissue transmission window (1600-1900 nm) by reviewing state of the art in ultrafast laser sources development. Finally, we summarise the most recent results in developing multiphoton endoscopes – a key element for clinical in vivo translation of photonics-based diagnostics.