The Galileo Near Infrared Mapping Spectrometer (NIMS) obtains spectral images in the wavelength range 0.7 to 5.2 μm with a spectral resolving power of approximately 200. This spectral range allows NIMS to sense cloud-reflected solar radiation, thermal emission produced in the deep atmosphere, and auroral emission from the thermosphere of Jupiter. Using 5 μm thermal emission spectroscopy, the amount of water vapor in the deep atmosphere, at approximately the (i to 8 bar level, is found to vary by a factor > 100. Deep atmosphere ammonia was also found to vary, with a spatial behavior different from that of water vapor. No evidence is found for a massive water cloud. Using reflected solar radiation in conjunction with thermal emission, two cloud layers are found, the upper at 0.5 bars and a lower one at 1-1.3 bars. The inferred absorption properties of these clouds are consistent with ammonia crystals (the upper cloud) and ammonium hydrosulfide particles (the lower cloud).