Background: Axonal damage is considered a major cause of disability in multiple sclerosis (MS) and may start early in the disease. Specific biomarkers for this process are of great interest. Objective: To study if cerebrospinal fluid (CSF) biomarkers for axonal damage reflect and predict disease progression already in the earliest stages of the disease, that is, in clinically isolated syndrome (CIS). Methods: We assessed CSF levels of neurofilament heavy (NFH), neurofilament light (NFL) and N-acetylaspartate (NAA) in 67 patients with CIS and 18 controls with neuropsychiatric diseases of non-inflammatory aetiology (NC). Patients with CIS underwent baseline magnetic resonance imaging (MRI) at 3T, and a follow-up MRI after 1 year was obtained in 28 of them. Results: Compared with NC, patients with CIS had higher NFH ( p=0.05) and NFL ( p<0.001) levels. No significant group differences were found for NAA. Patients’ NFH levels correlated with physical disability ( r=0.304, p<0.05) and with change in brain volume over 1 year of follow-up ( r=-0.518, p<0.01) but not with change in T2 lesion load. Conclusion: Our results confirm increased neurofilament levels already in CIS being related to the level of physical disability. The association of NFH levels with brain volume but not lesion volume changes supports the association of these markers with axonal damage.