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Background Autologous haematopoietic stem cell transplantation (AHSCT) has emerged as a highly effective treatment for relapsing-remitting multiple sclerosis (RRMS), though patient selection remains challenging. The degree to which disease-modifying therapies (DMTs) and procedure-related complications affect treatment outcomes is unclear. The objective of this study was to investigate the factors that might influence outcomes following AHSCT.Methods Data from the multicentre, retrospective cohort study Haematopoietic Stem Cell Transplantation for Treatment of Multiple Sclerosis in Sweden (AutoMS-Swe) were analysed, comprising 174 patients with RRMS who received AHSCT before 1 January 2020. Primary outcomes included inflammatory disease activity, confirmed disability worsening (CDW) and overall evidence of disease activity. Confirmed disability improvement was investigated as a secondary outcome. Associations between variables of interest and outcomes were assessed using univariable Cox proportional hazards models.Results Patients who received rituximab as the last DMT before AHSCT had a reduced hazard of inflammatory disease activity (HR 0.18, 95% CI 0.04 to 0.78). Epstein-Barr virus detection was associated with a higher hazard of inflammatory disease activity (HR 2.3, 95% CI 1.05 to 5.07). CDW was associated with longer disease durations (HR 1.09, 95% CI 1.00 to 1.19) and was negatively associated with gadolinium-enhancing lesions (HR 0.08, 95% CI 0.01 to 0.64). No CDW events occurred in treatment-naive patients.Conclusions Prior rituximab treatment appears to be protective against inflammatory activity after AHSCT. Disease duration and gadolinium-enhancing lesions are major determinants of disability following AHSCT.