Integrity of outer retinal bands among multiple sclerosis (MS) subtypes remains unclear, however alterations of thickness in retinal layers is well described. The objective of the study was to determine the alterations in the thickness of the inner and outer layers of the retina and the findings in both layers detected by optical coherence tomography (OCT) among patients with relapsing-remitting multiple sclerosis (RRMS) and secondary progressive multiple sclerosis (SPMS). A total of 132 eyes from 66 patients with multiple sclerosis (MS) (70 eyes from 35 patients with RRMS and 62 eyes from 31 patients with SPMS) and 72 eyes from 36 healthy controls were included in the study. The external structures of the retina, including the outer limiting membrane (ELM), ellipsoid zone (EZ), and interdigitation zone (IZ), were examined using OCT in RRMS, SPMS, and healthy control groups. The correlation of neurological disability expressed by the Expanded Disability Study Scale (EDSS) score, best-corrected visual acuity, and duration of disease among OCT parameters was also analyzed. In eyes, with no history of previous optic neuritis (ON), the macular nerve fiber layer, the internal plexiform layer of ganglion cells (GCIPL), and the total thickness of the retinal layer were thinner in the SPMS group than in the RRMS group (P < 0.05, in each comparison). EZ was more vulnerable among the three hyperreflective external retinal zones in the retina of patients with SPMS than in patients with RRMS (P = 0.016). Alterations in retinal thickness in MS are not limited to the inner layers of the retina and also occur in the outer structures of the retina.