Pain is by definition a subjective experience that affects individuals in dramatically different ways. Individual variation across many domains of the pain experience, such as sensitivity to noxious stimuli and propensity to develop chronic pain, has been observed. For omics researchers concerned with exploring the molecular mechanisms underlying these traits, suitable phenotyping approaches are needed. These methods should strike a balance between accurate and comprehensive assessment while minimizing cost, expense, and time, to make pain phenotyping feasible in large-scale omics studies. Validated diagnostic tools are available to assess pain intensity, location, sensory qualities, and other signs and symptoms associated with pain. Additional measures may be used to capture psychosocial and functional characteristics, such as anxiety, negative affect, and disturbances in sleep. Quantitative sensory testing (QST) procedures are recommended for exploring the function of nociceptive pathways and endogenous modulatory systems. The best path forward for the “pain-omics” research community is to adopt a collaborative approach incorporating consistent, rigorous, and mechanism-based phenotyping measures with current informatics technology.