Intervertebral disc degeneration (DD) is a cause of low back pain (LBP) in some individuals. However, while >30% of adults have DD, LBP only develops in a subset of individuals. To gain insight into the mechanisms underlying non-painful versus painful DD, human cerebrospinal fluid (CSF) was examined using differential expression shotgun proteomic techniques comparing healthy controls, subjects with non-painful DD, and patients with painful DD scheduled for spinal fusion surgery. Eighty-eight proteins were detected, 27 of which were differentially expressed. Proteins associated with DD tended to be related to inflammation (e.g. cystatin C) regardless of pain status. In contrast, most differentially expressed proteins in DD-associated chronic LBP patients were linked to nerve injury (e.g. hemopexin). Cystatin C and hemopexin were selected for further examination by ELISA in a larger cohort. While Cystatin C correlated with DD severity but not pain or disability, hemopexin correlated with pain intensity, physical disability and DD severity. This study demonstrates that CSF can be used to study mechanisms underlying painful DD in humans, and suggests that while painful DD is associated with nerve injury, inflammation itself is not sufficient to develop LBP.