Background: Individuals with immune-mediated inflammatory diseases, such as inflammatory bowel disease, multiple sclerosis and rheumatoid arthritis, are at increased risk for influenza and related complications. We examined and compared the uptake of influenza vaccination among people with and without these diseases, as well as the influence of psychiatric comorbidity on vaccine uptake., Methods: Using administrative data from Apr. 1, 1984, to Mar. 31, 2016, we conducted a retrospective matched cohort study in Manitoba, Canada. We matched persons 18 years of age or older who had a diagnosis of inflammatory bowel disease, multiple sclerosis or rheumatoid arthritis (the immune-mediated inflammatory disease cohorts) with persons who did not have these diagnoses (the control cohorts) on age, sex and region. We then identified cohort members with any mood or anxiety disorder (depression, anxiety disorders, bipolar disorder). We identified influenza vaccinations through billing codes. Using binomial regression, we modelled the difference in the proportion of the immune-mediated inflammatory disease and matched cohorts vaccinated annually, with adjustment for sociodemographic characteristics, comorbidity and immune therapy. We tested additive interaction effects between a person's cohort and presence of a mood or anxiety disorder., Results: We identified 32 880 individuals with 1 or more immune-mediated inflammatory diseases (10 148 with inflammatory bowel disease, 6158 with multiple sclerosis and 16 975 with rheumatoid arthritis) and a total of 164 152 controls. In fiscal year 2015, 8668 (41.3%, 95% confidence interval [CI] 40.6% to 42.0%) of the 20 982 persons with an immune-mediated inflammatory disease received an influenza vaccination, a rate higher than among controls (35 238 of 104 634; 33.7%, 95% CI 33.4% to 34.0%). After adjustment, participants with an immune-mediated inflammatory disease but no mood or anxiety disorder had 6.44% (95% CI 5.79% to 7.10%) greater uptake of vaccination than participants without such a disease. Among participants without an immune-mediated inflammatory disease, having a mood or anxiety disorder was associated with 4.54% (95% CI 4.20% to 4.89%) greater uptake of vaccination. However, we observed a subadditive interaction between immune-mediated inflammatory disease and psychiatric status (-1.38%, 95% CI -2.26% to -0.50%)., Interpretation: Uptake of influenza vaccination was consistently low in populations with immune-mediated inflammatory disease, and although psychiatric morbidity is associated with greater vaccine uptake by Manitobans, it negatively interacts with these diseases to reduce uptake. Changes in care delivery are needed to mitigate this gap in care., Competing Interests: Competing interests: For work outside the study reported here, Ruth Ann Marrie has received research funding from the Canadian Institutes of Health Research (CIHR), Research Manitoba, the Multiple Sclerosis Society of Canada, the Multiple Sclerosis Scientific Research Foundation, Crohn’s and Colitis Canada, the National Multiple Sclerosis Society and the Consortium of Multiple Sclerosis Centers; she has also participated in research funded by Roche and Biogen Idec (all funds to co-investigators). Jitender Sareen has received consulting fees from UpToDate and previously held stock in Johnson & Johnson. For work outside the study reported here, Scott Patten has received research funding from CIHR, the Hotchkiss Brain Institute and the Multiple Sclerosis Society of Canada (which includes contributions from Roche, Biogen and the Government of Alberta); he also holds the Cuthbertson and Fischer Chair in Pediatric Mental Health at the University of Calgary. Alexander Singer has received financial and in-kind support from an IBM/CIMVHR Advanced Analytics Grant and Calian Inc. For work outside the study reported here, Lisa Lix has received research funds from CIHR and the Arthritis Society. Carol Hitchon has received research funds for unrelated studies from UCB Canada and Pfizer. James Marriott has received grant funding from Roche (as site principal investigator for a clinical trial). Renée El-Gabalawy has received research funds for unrelated studies from University of Manitoba Start-Up Funds, the CIHR Chronic Pain Network, Health Sciences Centre foundation grant, Department of Anesthesia operating grant and the Tri-Agency New Frontiers in Research Fund. For activities unrelated to the current study, John Fisk has received research funds from CIHR, the Multiple Sclerosis Society of Canada, the Nova Scotia Health Authority Research Fund and the Dalhousie Medical Research Fund, as well as royalty fees from MAPI Research Trust. For activities unrelated to the current study, Charles Bernstein has received consultancy fees from Roche Canada, Mylan Pharmaceuticals and Takeda Canada; contract research funding from Pfizer, Janssen Canada and Roche; unrestricted educational or research grants from Abbvie Canada, Janssen Canada, Pfizer Canada, Takeda Canada, Sandoz and Medtronic Canada; speakers’ fees from Abbvie Canada, Janssen Canada, Pfizer Canada, Takeda Canada and Medtronic Canada; and has served on advisory boards for Abbvie Canada, Janssen Canada, Pfizer Canada, Takeda Canada, Sandoz, Amgen Canada, Bristol Myers Squibb Canada and Roche Canada. No other competing interests were declared., (© 2021 CMA Joule Inc. or its licensors.)