Background: People with substance use disorder have a high risk of SARS-CoV-2 infection and subsequent poor outcomes. Few studies have evaluated COVID-19 vaccine effectiveness among people with substance use disorder. We aimed to estimate the vaccine effectiveness of BNT162b2 (Fosun-BioNTech) and CoronaVac (Sinovac) against SARS-CoV-2 omicron (B.1.1.529) infection and related hospital admission in this population., Methods: We did a matched case-control study using electronic health databases in Hong Kong. Individuals diagnosed with substance use disorder between Jan 1, 2016, and Jan 1, 2022, were identified. People aged 18 years and older with SARS-CoV-2 infection from Jan 1 to May 31, 2022, and people with COVID-19-related hospital admission from Feb 16 to May 31, 2022, were included as cases and were matched by age, sex, and previous clinical history with controls from all individuals diagnosed with substance use disorder who attended the Hospital Authority health services: up to three controls for SARS-CoV-2 infection and up to ten controls for hospital admission. Conditional logistical regression was used to evaluate the association between vaccination status (ie, one, two, or three doses of BNT162b2 or CoronaVac) and the risk of SARS-CoV-2 infection and COVID-19-related hospital admission, adjusted for baseline comorbidities and medication use., Findings: Among 57 674 individuals with substance use disorder, 9523 people with SARS-CoV-2 infections (mean age 61·00 years, SD 14·90; 8075 [84·8%] males and 1448 [15·2%] females) were identified and matched to 28 217 controls (mean age 60·99 years, 14·67; 24 006 [85·1%] males and 4211 [14·9%] females), and 843 people with COVID-19-related hospital admissions (mean age 70·48 years, SD 14·68; 754 [89·4%] males and 89 [10·6%] females) were identified and matched to 7459 controls (mean age 70·24 years, 13·87; 6837 [91·7%] males and 622 [8·3%] females). Data on ethnicity were not available. We observed significant vaccine effectiveness against SARS-CoV-2 infection for two-dose BNT162b2 vaccination (20·7%, 95% CI 14·0-27·0, p<0·0001) and three-dose vaccination (all BNT162b2 41·5%, 34·4-47·8, p<0·0001; all CoronaVac 13·6%, 5·4-21·0, p=0·0015; BNT162b2 booster after two-dose CoronaVac 31·3%, 19·8-41·1, p<0·0001), but not for one dose of either vaccine or two doses of CoronaVac. Significant vaccine effectiveness against COVID-19-related hospital admission was detected after one dose of BNT162b2 vaccination (35·7%, 3·8-57·1, p=0·032), two-dose vaccination (both BNT162b2 73·3%, 64·3 to 80·0, p<0·0001; both CoronaVac 59·9%, 50·2-67·7, p<0·0001), and three-dose vaccination (all BNT162b2 86·3%, 75·6-92·3, p<0·0001; all CoronaVac 73·5% 61·0-81·9, p<0·0001; BNT162b2 booster after two-dose CoronaVac 83·7%, 64·6-92·5, p<0·0001), but not after one dose of CoronaVac., Interpretation: For both BNT162b2 and CoronaVac, two-dose or three-dose vaccination was protective against COVID-19-related hospital admission and the booster dose provided protection against SARS-CoV-2 infection among people with substance use disorder. Our findings confirm the importance of booster doses in this population during the period dominated by the omicron variant., Funding: Health Bureau, the Government of the Hong Kong Special Administrative Region., Competing Interests: Declaration of interests BJC reported receiving consulting fees from AstraZeneca, Fosun Pharma, GlaxoSmithKline, Haleon, Moderna, Pfizer, Roche, and Sanofi Pasteur outside the submitted work. DJC reported receiving personal fees from Seqirus, Lundbeck, and Servier, grants from Boehringer Ingelheim, the National Health and Medical Research Council (Australia), Milken Institute, and Psyche Foundation, is a founder of and holds 50% of the intellectual property for the Optimal Health Program, is part owner (5%) of Clarity Healthcare, and serves as an advisory board chair of an Australian not-for-profit institute specialising in psychedelic medicines research, outside the submitted work. CSLC reported receiving grants from the Health Bureau of the Government of the Hong Kong Special Administrative Region during the conduct of the study; grants from Hong Kong Innovation and Technology Commission, Hong Kong Research Grants Council, Pfizer, Amgen, MSD, and IQVIA; and consultancy fees from Primevigilance outside the submitted work. FTTL reported support from the RGC Postdoctoral Fellowship under the Hong Kong Research Grants Council and received research grants from the Health Bureau of the Government of the Hong Kong Special Administrative Region outside the submitted work. XL reported receiving research grants from the Health Bureau of the Government of the Hong Kong Special Administrative Region, Research Grants Council Early Career Scheme, Research Grant Council, and Research Impact Fund; research and educational grants from Janssen and Pfizer; internal funding from the University of Hong Kong; and consultancy fees from Merck Sharp & Dohme, unrelated to this work; and payment or honoraria for lectures, presentations, speakers bureaus, manuscript writing, or educational events from Pfizer, outside the submitted work. EYFW reported receiving research grants from the Health Bureau of the Government of the Hong Kong Special Administrative Region, and the Hong Kong Research Grants Council, and National Natural Science Foundation of China outside the submitted work. CKHW reported receipt of grants from the General Research Fund, Research Grant Council, the Government of Hong Kong, EuroQol Research Foundation, AstraZeneca, and Boehringer Ingelheim, all outside the submitted work. JFH reported receiving grants from UK Research and Innovation, Wellcome Trust, National Institute for Health and Care Research University College London Hospitals Biomedical Research Centre, and National Institute for Health and Care Research Applied Research Collaboration North Thames during the conduct of the study; personal fees from Wellcome Trust and juli Health; and patent pending for juli Health, outside the submitted work. ICKW reported receiving research funding from Amgen, Bristol Myers Squibb, Pfizer, Janssen, Bayer, GlaxoSmithKline, Novartis, the Hong Kong Research Grants Council, the Hong Kong Health and Medical Research Fund, the Hong Kong Innovation and Technology Commission, the National Institute for Health and Care Research, the European Commission, and the Australian National Health and Medical Research Council; and receiving expert testimony payment consultancy fees from WHO and IQVIA; and is an independent non-executive director of Jacobson Medical in the Hong Kong Court of Final Appeal, outside the submitted work. EWC reported receiving grants from the National Natural Science Foundation of China during the conduct of the study; non-financial support from Wellcome Trust; grants from Research Grants Council, Research Fund Secretariat of the Health Bureau (via the Health and Medical Research Fund), National Health and Medical Research Council (Australia), Narcotics Division of the Security Bureau of the Hong Kong Special Administrative Region, Amgen, AstraZeneca, Bayer, Bristol Myers Squibb, Janssen, Pfizer, Takeda, Novartis, and RGA Reinsurance Company; and personal fees from Pfizer, AstraZeneca, Novartis, Pfizer, and the Hong Kong Special Administrative Region Hospital Authority outside the submitted work. All other authors declare no competing interests., (Copyright © 2023 Elsevier Ltd. All rights reserved.)