The interaction of intense femtosecond laser pulses with transparent materials is a topic that has caused great interest of scientists over the past two decades. It will continue to be a fascinating field in the coming years. This is because many challenging fundamental problems have not been solved, especially concerning the interaction of strong, ultra-short electromagnetic pulses with matter, and also because potential advanced technologies will emerge due to the impressive capability of the intense femtosecond laser to create new material structures and hence functionalities. When femtosecond laser interacts with matter, a large amount of energy will be released during an ultra-short period of time, resulting in extremely high energy intensity. This opens the avenue to explore new light-matter interacting phenomena, investigate the details of the dynamical processes of the light-matter interaction, and fabricate various integrated micro-devices. In recent years we have witnessed exciting development in understanding and applying ferntosecond laser induced phenomena in transparent materials. The interaction of femtosecond laser pulses with transparent materials relies on non-equilibrium process with photon beams and this provides new access to create materials and micro-devices that cannot be obtained by other means. Understanding of the physical mechanisms of many induced phenomena is extremely challenging. The aim of this review is to present a critical overview of the current state of the art in studying femtosecond laser induced various phenomena in transparent materials, including their physical and chemical mechanisms, the applications and limitations as well as the future research trends. The first part of the review presents the basics of femtosecond laser systems, important parameters influencing the femtosecond laser interaction with transparent materials, and a brief description of various energy transfer processes in materials during femtosecond laser irradiation, The second part will give an account on various phenomena such as multiphoton excited upconversion luminescence, long lasting phosphorescence, formation of color centers, valence state change, precipitation of nanoparticles and nanocrystals, microvoids, polarization-dependent and periodic surface structures, refractive index change, polymerization and air-bubble formation. The third part describes recently observed "anomalous" phenomena such as induced birefringence, nanogratings, nanovoid arrays, migration of ions, nonreciprocal photosensitivity, high pressure crystalline phase, and their underlying mechanisms, and their potential prospects as a new tool for photonic technology development. The final part points out the major challenges and future research trends in this promising field. (C) 2015 Elsevier Ltd. All rights reserved.