Background: Employing a rebaselining concept may reduce noise in retinal layer thinning measured by optical coherence tomography (OCT)., Methods: From an ongoing prospective observational study, we included patients with relapsing multiple sclerosis (RMS), who had OCT scans at disease-modifying treatment (DMT) start (baseline), 6-12 months after baseline (rebaseline), and ⩾12 months after rebaseline. Mean annualized percent loss (aL) rates (%/year) were calculated both from baseline and rebaseline for peripapillary-retinal-nerve-fiber-layer (aLpRNFL baseline /aLpRNFL rebaseline ) and macular-ganglion-cell-plus-inner-plexiform-layer (aLGCIPL baseline /aLGCIPL rebaseline ) by mixed-effects linear regression models., Results: We included 173 RMS patients (mean age 31.7 years (SD 8.8), 72.8% female, median disease duration 15 months (12-94) median baseline-to-last-follow-up-interval 37 months (18-71); 56.6% moderately effective DMT (M-DMT), 43.4% highly effective DMT (HE-DMT)). Both mean aLpRNFL baseline and aLGCIPL baseline significantly increased in association with relapse (0.51% and 0.26% per relapse, p < 0.001, respectively) and disability worsening (1.10% and 0.48%, p < 0.001, respectively) before baseline, but not with DMT class. Contrarily, neither aLpRNFL rebaseline nor aLGCIPL rebaseline was dependent on relapse or disability worsening before baseline, while HE-DMT significantly lowered aLpRNFL rebaseline (by 0.31%, p < 0.001) and aLGCIPL rebaseline (0.25%, p < 0.001) compared with M-DMT., Conclusions: Applying a rebaselining concept significantly improves differentiation of DMT effects on retinal layer thinning by avoiding carry-over confounding from previous disease activity., Competing Interests: Declaration of Conflicting InterestsThe author(s) declared the following potential conflicts of interest with respect to the research, authorship, and/or publication of this article: Gabriel Bsteh has participated in meetings sponsored by, received speaker honoraria or travel funding from Biogen, Celgene/BMS, Lilly, MedWhizz, Merck, Novartis, Roche, Sanofi Genzyme and Teva, and received honoraria for consulting Biogen, Celgene/BMS, Merck, Novartis, Roche, Sanofi Genzyme, and Teva. He has received unrestricted research grants from Celgene/BMS and Novartis.Harald Hegen has participated in meetings sponsored by, received speaker honoraria or travel funding from Bayer, Biogen, Bristol Myers Squibb, Horizon, Merck, Novartis, Sanofi Genzyme, Siemens and Teva, and received honoraria for consulting Biogen, Bristol Myers Squibb, Novartis, Roche, Sanofi Genzyme, and Teva. He is associate editor of Frontiers in Neurology.Nik Krajnc has participated in meetings sponsored by, received speaker honoraria or travel funding from Alexion, BMS/Celgene, Janssen-Cilag, Merck, Novartis, Roche and Sanofi Genzyme and held a grant for a Multiple Sclerosis Clinical Training Fellowship Programme from the European Committee for Treatment and Research in Multiple Sclerosis (ECTRIMS).Fabian Föttinger has nothing to disclose.Patrick Altmann has participated in meetings sponsored by, received speaker honoraria or travel funding from Biogen, Merck, Roche, Sanofi Genzyme and Teva, and received honoraria for consulting from Biogen. He received a research grant from Quanterix International and was awarded a combined sponsorship from Biogen, Merck, Sanofi Genzyme, Roche, and Teva for a clinical study.Michael Auer has participated in meetings sponsored by, received speaker honoraria or travel funding from Biogen, Merck, Novartis, Sanofi Genzyme and Horizon Therapeutics.Klaus Berek has participated in meetings sponsored by and received travel funding from Biogen, Roche, Sanofi Genzyme, and Teva.Barbara Kornek has received honoraria for speaking and for consulting from Biogen, BMS-Celgene, Johnson & Johnson, Merck, Novartis, Roche, Teva, and Sanofi Genzyme outside of the submitted work. No conflict of interest with respect to the present study.Fritz Leutmezer has participated in meetings sponsored by, received speaker honoraria or travel funding from Actelion, Almirall, Biogen, Celgene, Johnson & Johnson, MedDay, Merck, Novartis, Roche, Sanofi Genzyme, and Teva, and received honoraria for consulting Biogen, Celgene, Merck, Novartis, Roche, Sanofi Genzyme, and Teva.Stefan Macher declares no conflict of interest relevant to this study.Tobias Monschein has participated in meetings sponsored by or received travel funding from Biogen, Merck, Novartis, Roche, Sanofi Genzyme, and Teva.Markus Ponleitner has participated in meetings sponsored by, received speaker or consulting honoraria or travel funding from Amicus, Merck, Novartis and Sanofi Genzyme.Paulus Rommer has received honoraria for consultancy/speaking from Alexion/Astra Zeneca, Allmiral, Amgen/Horizon, Amicus, Biogen, Merck, Novartis, Roche, Sandoz, Sanofi has received research grants from Amicus, Biogen, Merck, and Roche.Christiane Schmied declares no conflict of interest relevant to this study.Karin Zebenholzer received speaking honoraria or travel grants from Biogen, Celgene/BMS, Novartis, and Sanofi Genzyme.Gudrun Zulehner has participated in meetings sponsored by or received travel funding from Biogen, Merck, Novartis, Roche, Sanofi Genzyme, and Teva.Tobias Zrzavy has participated in meetings sponsored by or received travel funding from Biogen, Merck, Novartis, Roche, Sanofi Genzyme, and Teva.Florian Deisenhammer has participated in meetings sponsored by or received honoraria for acting as an advisor/speaker for Alexion, Almirall, Biogen, Celgene, Merck, Novartis, Roche, and Sanofi Genzyme. His institution received scientific grants from Biogen and Sanofi Genzyme.Franziska Di Pauli has participated in meetings sponsored by, received honoraria (lectures, advisory boards, consultations) or travel funding from Biogen, Celgene BMS, Horizon, Johnson & Johnson, Merck, Novartis, Sanofi Genzyme, Teva, and Roche. Her institution has received research grants from Roche.Berthold Pemp has received honoraria for consulting from Novartis, has received honoraria for advisory boards/consulting from Chiesi and GenSight, and has received speaker honoraria from Novartis, Chiesi, and Santen.Thomas Berger has participated in meetings sponsored by and received honoraria (lectures, advisory boards, consultations) from pharmaceutical companies marketing treatments for MS: Allergan, Bayer, Biogen, Bionorica, BMS/Celgene, Genesis, GSK, GW/Jazz Pharma, Horizon, Janssen-Cilag, MedDay, Merck, Novartis, Octapharma, Roche, Sandoz, Sanofi Genzyme, Teva, and UCB. His institution has received financial support in the past 12 months by unrestricted research grants (Biogen, Bayer, BMS/Celgene, Merck, Novartis, Roche, Sanofi Genzyme, Teva) and for participation in clinical trials in multiple sclerosis sponsored by Alexion, Bayer, Biogen, Merck, Novartis, Octapharma, Roche, Sanofi Genzyme, and Teva.