SARS COV 2 is the virus responsible for COVID-19, a disease that has been blamed for inducing or exacerbating symptoms in patients with autoimmune diseases. Crohn's disease (CD) is an inflammatory bowel disease that affects genetically susceptible patients who develop an abnormal mucosal immune response to the intestinal microbiota. Patients who underwent Hematopoietic Stem cell Transplantation are considered at risk for COVID-19. The objective of this report was to describe for the first time the impact of COVID-19 in a group of 50 patients with Crohn's Disease (CD, 28 females, and 22 male) with a mean age of 38 years, previously submitted to Autologous, non-myeloablative, Hematopoietic Stem Cell Transplantation (Auto HSCT) between 2013 and 2021. In this series, 19 patients were diagnosed with positive COVID-19. In two (2) patients there was a report of the occurrence of two infectious episodes. Parameters related to HSCT, such as time elapsed since the procedure, vaccination status, CD status before and after infection, and clinical manifestations resulting from COVID-19, were evaluated. Among the patients with COVID-19, in three, submitted to Auto HSCT less than six (6) months ago, there was a change in the CD status, and one of them, in addition to the CD symptoms, started to present thyroid impairment with positive anti-TPO. Only one of the patients required hospitalization for five days to treat COVID-19 and remained in CD clinical remission. Nine patients reported late symptoms that may be related to COVID-19. There were no deaths, and the statistical evaluation of the series of COVID-19 patients after HSCT and those who did not present an infectious episode did not present significant data regarding the analyzed parameters. Despite the change in CD status in three patients and the presence of nine patients with late symptoms, we can conclude that there was no significant adverse impact concerning COVID-19 in the evaluated patients who underwent HSCT to treat CD.