We explored morphological as well as functional and clinical markers of the vision processing in a cross-sectional study of subjects with Clinically Isolated Syndrome (CIS), often an early stage of the multiple sclerosis. Eighteen subjects (28 [19–47] years, 13 females) were examined within 3 years from the event. Recorded was RNFL thickness, pattern-reversal and motion-onset VEPs (P-VEPs and M-VEPs), low and high contrast Visual Acuity (VA). While the better eyes exhibited the only relevant correlation between age and latency of M-VEPs ( r = −0.59, p = 0.012), the worse eyes exhibited also correlation between the disease duration and latency of P-VEPs ( r = −0.66, p = 0.004) and M-VEPs ( r = −0.54, p = 0.021). Correlations of functional and clinical parameters to an average thickness of the RNFL or to the EDSS did not pass the significance level. In a pilot group of 18 CIS patients we did not find any relationship between clinical parameters and the RNFL, while the functional markers (P-VEP and M-VEP) correlated to the disease duration and seemingly paradoxically improved with the time. These findings confirm superior sensitivity of the functional examination.