An infection of SARS-CoV-1, the causative agent of Severe Acute Respiratory Syndrome (SARS), may be followed by long-term clinical sequala. We hypothesized a greater 20-year multimorbidity incidence in people hospitalized for SARS-CoV-1 infection than those for influenza during similar periods. We conducted a retrospective cohort study using a territory-wide public healthcare database in Hong Kong. All patients aged ≥15 hospitalized for SARS in 2003 or influenza in 2002 or 2004 with no more than one of 30 listed chronic disease were included. Demographics, clinical history, and medication use were adjusted for in the inverse-probability-of-treatment-weighted Poisson regression analyses. We identified 1255 hospitalizations for SARS-CoV-1 infection and 687 hospitalizations for influenza. Overall crude multimorbidity incident rates were 1.5 per 100 person-years among SARS patients and 5.6 among influenza patients. Adjusted multimorbidity incidence rate ratio (IRR) was estimated at 0.78 [95% confidence interval (CI), 0.70-0.86) for SARS patients compared with influenza patients. Analysis by follow-up period shows a potentially greater risk among SARS patients in the first year of follow-up (IRR 1.33, 95% CI 0.97-1.84), with the risk in influenza patients increasing in subsequent years. Subgroup analyses by age and sex showed consistent results with the main analysis that SARS-CoV-1 infection was not followed by a higher incidence of multimorbidity than influenza. Notable differences in the patterns of multimorbidity were identified between the two arms. To conclude, we found no evidence of a higher multimorbidity incidence after hospitalization for SARS than for influenza over the long-term.