The inner regions of protoplanetary disks are thought to be the most active regions for planet formation and thus potentially hold the key to understanding the formation of solar systems like our own. I will present a large, comprehensive survey of rovibrational CO line emission at 4.7 micron from 70 protoplanetary disks and 22 embedded protostars, obtained with CRIRES on the ESO Very Large Telescope at the highest available spectral resolving power (R=95,000, v=3.2 km/s). The CO fundamental band is a well-known tracer of warm gas in the inner, planet-forming regions of gas-rich disks around young stars, with the lines formed primarily in the super-heated surfaces of the disks at radii of 0.1--10 AU. The presence of warm emission from young protostars allows examination of the inner few AU region which is difficult to observe due to the dense molecular envelope. In older class II disks, the presence of line emission is found to be ubiquitous as long as the disks contain warm dust. Our high resolution data provide new insight into the complex kinematics of the gas with observational signatures of disks, winds, outflows and molecular clouds. The sensitivity to weak isotopologues provides new constraints on the surface layer temperature structure. Detailed knowledge of gas in the inner regions of disks is a key component needed to determine the evolutionary process from embedded protostars to circumstellar disks to planetary systems.