UNLABELLED: Heated tobacco products (THPs) are increasingly promoted as potential harm reduction tools, offering an alternative to traditional cigarettes. Despite these claims, understanding of their toxicological impact on respiratory health and associated microbial communities is limited. Comprehensive investigations are needed to elucidate the biological mechanisms and potential health implications associated with their use. METHODS: This study evaluated the toxicological effects of aerosols produced by THPs (IQOS 3 Duo with Heets "Sienna Selection") in comparison to conventional cigarette smoke (1R6F). Antibacterial activity was evaluated using and as representative species of the respiratory microbiota through agar diffusion assays and MIC/MBC determinations. Cytotoxicity was assessed in human lung fibroblast cells (MRC5) through the neutral red uptake (NRU) assay, whereas mutagenicity was investigated using the Ames test. RESULTS: THP aerosols demonstrated the ability to inhibit the growth of both and , exerting bacteriostatic effects at lower concentrations and bactericidal effects at higher concentrations. While these antibacterial effects might initially seem beneficial against pathogens such as , they raise concerns about the potential disruption of the respiratory microbial balance, particularly in relation to . Despite these microbiological effects, THP aerosols demonstrated minimal cytotoxicity on human lung fibroblasts and lacked detectable mutagenic activity, contrasting with the significant cytotoxicity and mutagenicity caused by cigarette smoke. CONCLUSIONS: THPs present a reduced short-term toxicological profile compared with conventional cigarettes; however, their effects on respiratory microorganisms deserve attention. The observed inhibition of commensal bacteria highlights the need to explore potential changes in the microbial ecosystem that could affect respiratory health. These findings highlight the need for additional studies to evaluate the long-term effect of THP use on respiratory microbiota and the stability of the overall microbial ecosystem.