Intervertebral disc herniation is an important and common pathology in both humans and dogs. Although imaging diagnostics (CT and MR) is the main routine method of diagnosing IVDH, it can not be used to detect the early stage of the disease, as well as to explain the molecular processes and protein interactions involved in the pathophysiology of the disease. In this light, to decipher molecules involved in pathophysiology of IVDH, a qualitative and quantitative proteomic analysis of the cerebrospinal fluid of 6 healthy dogs as well as 9 dogs with IVDH was performed using mass spectrometry-based proteomics. Using the SEQUEST algorithm integrated within Proteome Discoverer software, 205 cerebrospinal fluid proteins were identified, 75 of which were differentially expressed. Gene ontology indicated that the obtained proteins are involved in calcium binding, oxidative stress, lipid metabolism, collagen polymerization, inflammatory processes and immune response. Proteins with diagnostic potential involved in neuropathic pain, myelination, neuroinflammation and immune response were identified herein. Their clinical application of those molecules would facilitate the diagnosis of IVHD in the early stages of the disease. One of the differentially expressed proteins, more precisely paraoxonase 1 (PON1), which plays a key role in maintaining the homeostatic balance of the intervertebral disc, has been analytically validated, but for its clinical application in IVDH diagnostics, validation on a larger number of patients is required.