Multiphoton microscopy (MPM) is the method of choice for investigating cells and cellular functions in deep tissue sections and organs. Here we present the setup and applications of infrared-(IR-)MPM using excitation wavelengths above 1080 nm. IR-MPM enables the use of red fluorophores and fluorescent proteins, doubles imaging depth, improves second harmonic generation of tissue structures, and strongly reduces phototoxicity and photobleaching, compared with conventional MPM. Furthermore, it still provides subcellular resolution at depths of several hundred micrometers and thus will enhance long-term live cell and deep tissue microscopy.