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Background/Aims: Vaccination against severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is one of the best policies to control COVID-19 pandemic. The serological response to COVID-19 vaccination in Taiwanese patients with different comorbidities is elusive. Methods: Uninfected subjects who received 3 doses of mRNA vaccines (BNT162b2 [Pfizer-BioNTech, BNT] and mRNA-1273 [Moderna]), viral vector-based vaccines (ChAdOx1-S (AZD1222, AZ) or protein subunit vaccines (Medigen COVID-19 vaccine) were prospectively enrolled. The SARS-CoV-2-IgG spike antibody level was determined within three months after the 3rd dose of vaccination. The Charlson Comorbidity Index (CCI) was applied to determine the association between vaccine titers and underlying comorbidities. Results: A total of 824 subjects were enrolled in the current study. The proportions of CCI scores of 0–1, 2–3 and > 4 were 52.8% (n = 435), 31.3% (n = 258) and 15.9% (n = 131), respectively. The most commonly used vaccination combination was AZ–AZ–Moderna (39.2%), followed by Moderna–Moderna–Moderna (27.8%). The mean vaccination titer was 3.11 log BAU/mL after a median of 48 days after the 3rd dose. Factors associated with potentially effective neutralization capacity (IgG level ≥ 4160 AU/mL) included age ≥ 60 years (odds ratio [OR]/95% confidence interval [CI]: 0.50/0.34–0.72, P < 0.001), female sex (OR/CI: 1.85/1.30–2.63, P = 0.001), Moderna–Moderna-based vaccination (compared to AZ–AZ-based vaccination, OR/CI: 6.49/3.90–10.83, P < 0.001), BNT–BNT-based vaccination (compared to AZ–AZ-based vaccination, OR/CI: 7.91/1.82–34.3, P = 0.006) and a CCI score ≥ 4 (OR/CI: 0.53/0.34–0.82, P = 0.004). There was a decreasing trend in antibody titers with increasing CCI scores (trend P < 0.001). Linear regression analysis revealed that higher CCI scores (β: − 0.083; 95% CI: − 0.094–0.011, P = 0.014) independently correlated with low IgG spike antibody levels. Conclusions: Subjects with more comorbidities had a poor serological response to 3 doses of COVID-19 vaccination. [ABSTRACT FROM AUTHOR]