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Aims: To identify clinical symptoms and nursing interventions for stem cell therapy in autoimmune diseases., Design: This is a retrospective, cross-sectional study., Methods: This study was undertaken with patients diagnosed with type 1 diabetes or multiple sclerosis, undergoing autologous haematopoietic stem cell transplantation from January 2004 - December 2018. Data were registered in a questionnaire, taken during the conditioning regimen comprising cyclophosphamide and rabbit anti-thymocyte globulin. Descriptive statistics and Fisher's exact test were used for data analysis., Results: There were 68 and 23 patients in the multiple sclerosis and type 1 diabetes groups respectively. Skin rash, nausea, vomiting and fever were more frequent and diverse in the type 1 diabetes group. Steroids were used as prophylaxis for anti-thymocyte globulin-associated allergic reactions in 97% of multiple sclerosis patients. Most of the identified symptoms and nursing interventions were more associated with one or other disease group (p < .05) and were more frequent in the type 1 diabetes group., Conclusion: Patients with autoimmune diseases who underwent stem cell therapy present differences in their repertoire of adverse events and require disease-specific nursing actions., Impact: Our results may enable nurses to establish transplant and disease-specific guidelines to improve prevention and management of adverse events and therefore optimize patient care and therapeutic success., (© 2020 John Wiley & Sons Ltd.)