Intervertebral disc (IVD) degeneration and associated low back pain (LBP) remains a major burden to our society without a significant improvement in treatment strategies or patient’s quality of life. While the recent cell-transplantation studies for treatment of degenerative disc disease showed promising results, to better gauge the success and functional outcomes of these therapies, it is crucial to understand if transplanted cells give rise to healthy nucleus pulposus (NP) tissue. NP cell phenotype is unique and is defined by expression of a characteristic set of markers that reflect their specialized physiology and function. This review summarizes phenotypic markers that mirror unique physiology and function of NP cells and their progenitors and should be considered to measure outcomes of cell-based therapies to treat disc degeneration.