There remain many fundamental unanswered questions about protoplanetary disks, including how (and if?) they form planets, how mass is transferred through the disk and onto the star, and how they ultimately disperse. Also, a major goal of protoplanetary disk studies is to understand the relationship between disk properties and the physical and chemical properties of planetary systems. IR molecular spectroscopy is a particularly powerful tool for probing the conditions and physical process in protoplanetary disks, which are too small and close to their parent stars to be imaged with ease. I will discuss the suite of infrared molecular transitions observed to date, which highlight the following three techniques of IR spectroscopy. Firstly, line shapes and strengths can be used as tracers of disk physics, including volatile condensation/evaporation, photo-processes, grain growth and turbulence. Secondly, observations of multiple molecular abundances provide constraints for disk chemical models, which may ultimately help explain the great diversity of planetary bodies. Finally, resolved line shapes and spectro-astrometry provide a means to study disk structure on extremely small size scales. Because IR observations are typically sensitive to radii of a few AU or smaller, the processes and structures being probed are relevant to the birth and growth of terrestrial and giant planets. Recent results that I will highlight include the discovery of a multitude of molecules in disks around sun-like stars (including H2O, OH, HCN, C2H2 and CO2), with detection rates that depend on stellar mass, constraints on gas mass and location in transitional disks, detection and characterization of ‘snow lines’, measurements of inner disk rims, and detections of inner disk asymmetries. I will also discuss how IR spectroscopy will remain relevant even with the emergence of facilities such as ALMA, as it allows us to connect the conditions in terrestrial-planet-forming regions with those in the cold outer reaches of disks, and to better construct a comprehensive understanding of the nature of protoplanetary disks.