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Background: The rising use of electronic cigarettes (e-cigarettes) has become a significant public health issue. While e-cigarettes are seen as a safer alternative to traditional smoking, they may still expose users to toxic chemicals that could adversely affect oral health. This study aims to investigate the cytomorphometric changes in buccal mucosal cells among different smoking groups, including e-cigarette vapers, traditional smokers of varying intensities, and non-smokers, and to correlate these findings with salivary thiocyanate levels, a biomarker for cyanide exposure. Methods: A cross-sectional study included 73 male participants (aged 18-50 years) conducted in Al Muqdadiyah City, Diyala Governorate, Iraq. The participants were classified into five groups: electronic cigarette vapers (ECV, n=25), heavy regular cigarette smokers (Heavy RCS, n=12), moderate regular cigarette smokers (Moderate RCS, n=12), mild regular cigarette smokers (Mild RCS, n=12), and non-smoking controls (NSC, n=12). Salivary thiocyanate levels were assessed using atomic absorption spectrophotometry. Oral exfoliative cytology was utilized, with the cytological evaluation of the buccal mucosal smears focusing on nuclear abnormalities, including total micronuclei (MN), micronucleated cells (MN cells), binucleated (BN) cells, nuclear buds (NB), karyorrhectic (KR) cells, karyolytic (KL) cells, and pyknotic (PK) cells, which were stained using Papanicolaou (PAP) staining. Statistical analyses were performed for group comparisons and correlation tests. Results: Mean salivary thiocyanate levels in heavy RCS and e-cigarette vapers (5.51 ± 0.153 mM/L and 3.674 ± 0.422 mM/L) were higher than those in non-smokers (1.145 ± 0.15 mM/L), showing a highly significant difference (p=0.011) in thiocyanate levels. Additionally, the results indicated a significant increase in all nuclear abnormalities among smokers and e-cigarette users compared to non-smokers (P < 0.05). Heavy smokers displayed the most pronounced cytological changes, followed by e-cigarette users, moderate smokers, and mild smokers. However, the correlation between salivary thiocyanate and cytomorphometric changes was weak and inconsistent across all study groups. Conclusion: This study shows that e-cigarette use causes significant oral cellular damage comparable to moderate cigarette smoking, challenging the perception of e-cigarettes as safe alternatives. Both smoking types increased salivary thiocyanate levels and nuclear abnormalities in buccal cells. The weak correlation between biomarkers and cellular damage suggests multiple assessment tools are needed. These findings demonstrate that e-cigarettes pose substantial oral health risks and are not harmless.