Functional gastrointestinal disorders such as functional dyspepsia (FD) and irritable bowel syndrome (IBS) are stress-associated. The COVID-19 pandemic, which has been rampant since 2020, has caused anxiety and stress in the population. Distancing measures to combat the pandemic have affected mental health. Our objective was to examine the impact of the 3rd lockdown in Germany in December 2020 and January 2021 on the apprehension of patients with FD and IBS.Patients diagnosed with FD or IBS treated in a tertiary or primary care hospital in the South of Baden-Württemberg in 2020 voluntarily participated in an anonymous online survey. Questions about concomitant diseases, concern about COVID-19 and stress perception were answered.A total of 106 patients (♀=67, ♂=38, 1 diverse) participated in the survey. Of these, 16 had FD (♀=9, ♂=6, diverse=1), 80 had IBS (♀=52, ♂=28), and 10 had both (♀=6, ♂=4). The average age was 43.6 years. Depressive and anxiety disorders were most frequently reported comorbidities in both the FD (25% each) and IBS group (20% each), followed by joint wear and tear (FD: 13%, RDS: 14%). In a direct comparison of participants with FD and IBS, those with IBS showed significantly higher scores for an increase in gastrointestinal (GI) symptoms during the pandemic (p=0.007), more frequent presentation to a physician during the pandemic, and greater social withdrawal due to GI symptoms (p=0.05). In direct comparison, those with IBS showed higher scores for fear that vaccination against COVID-19 would adversely affect GI symptoms compared to FD (p=0.05).In times of the pandemic, interdisciplinary collaboration in the care of patients with FD or IBS seems more necessary than ever to address concerns and provide good patient care.