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Abstract Scientific evidence about genetic and molecular changes in oral squamous cell carcinoma (OSCC) among smokers and non-smokers is inconclusive. This systematic review and meta-analysis assessed the effects of tobacco on the DNA of individuals with OSCC based on protein mutations. Electronic searches were conducted on PubMed, Ovid, Web of Science, and Scopus to identify observational studies published up to January/2022. The Joanna Briggs Institute tool was used for the critical appraisal of studies. The certainty of the evidence was evaluated. Twenty-three studies assessing 4,060 individuals (2,967 smokers vs. 1,093 non-smokers) were included in this review. Fifteen groups of proteins/genes were investigated. Analysis of the quality of articles revealed low risk of bias in most studies. The certainty of the evidence was very low. The meta-analysis confirmed no significant difference between smokers and non-smokers with respect to damage to GSTM1 (OR: 0.60; 95%CI: 0.30–1.18), GSTT1 (OR: 1.18; 95%CI:0.49–2.83), hydrolase proteins (Ku70 and Ku80) (OR: 0.74; 95%CI: 0.18–3.05), and transferase proteins (GSTM1, GSTT1, GSTM3) (OR: 0.74; 95%CI: 0.47–1.18). Most of the studies included showed that smokers are more likely to exhibit genetic instability. However, the meta-analysis revealed that smokers do not necessarily have more genetic alterations in the DNA than non-smokers. (OSCC nonsmokers non inconclusive metaanalysis meta analysis mutations PubMed Ovid Science January2022 January 2022 January/2022 evaluated Twentythree Twenty three 4060 4 060 4,06 2,967 2967 2 967 (2,96 vs 1093 1 093 1,09 proteinsgenes genes investigated GSTM OR (OR 0.60 0 60 95%CI 95CI CI 95 0.30–1.18, 030118 0.30–1.18 , 30 18 0.30–1.18) GSTT 1.18 118 95%CI0.49–2.83, 95CI049283 0.49–2.83 49 83 95%CI:0.49–2.83) Ku70 Ku (Ku7 Ku80 0.74 074 74 0.18–3.05, 018305 0.18–3.05 3 05 0.18–3.05) GSTM1, (GSTM1 GSTM3 0.47–1.18. 047118 0.47–1.18 . 47 0.47–1.18) instability However nonsmokers. smokers. January202 202 January/202 406 06 4,0 2,96 296 96 (2,9 109 09 1,0 0.6 6 9 03011 0.30–1.1 1.1 11 CI0 95%CI0.49–2.83 95CI04928 049283 0.49–2.8 8 95%CI:0.49–2.83 Ku7 (Ku Ku8 0.7 07 7 01830 0.18–3.0 (GSTM 04711 0.47–1.1 January20 20 January/20 40 4, 2,9 29 (2, 10 1, 0. 0301 0.30–1. 1. 95%CI0.49–2.8 95CI0492 04928 0.49–2. 95%CI:0.49–2.8 0183 0.18–3. 0471 0.47–1. January2 January/2 2, (2 030 0.30–1 95%CI0.49–2. 95CI049 0492 0.49–2 95%CI:0.49–2. 018 0.18–3 047 0.47–1 January/ ( 03 0.30– 95%CI0.49–2 95CI04 049 0.49– 95%CI:0.49–2 01 0.18– 04 0.47– 0.30 95%CI0.49– 95CI0 0.49 95%CI:0.49– 0.18 0.47 0.3 95%CI0.49 0.4 95%CI:0.49 0.1 95%CI0.4 95%CI:0.4 95%CI0. 95%CI:0. 95%CI0 95%CI:0