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Many women report embarrassment as the cause for their avoidance of routine gynaecological screening appointments. Methods of self-collection of bio samples would perhaps encourage women to participate in routine screening programs. The vaginal microbiome plays a key role in women’s health and reproductive function. Microbial disturbances can result in the loss of lactobacillus dominance, also known as dysbiosis, associated with an increased risk of contracting sexually transmitted infections (STIs), pregnancy complications and infertility. Our primary aim was to determine if vaginal microbiome screening results are comparable between two methods for self-collected sample acquisition: tampons and lower vaginal swabs (LVSs). Secondary aims included the assessment of the effect of pre-analytic storage on the data (to streamline processing), the prevalence of dysbiosis and the acceptability of the tampons to the participants. Statistical analysis revealed no significant difference in the microbiome data, from tampons versus LVSs or fresh versus frozen samples. The prevalence of dysbiosis in this population of healthy volunteers was 42.9%. The questionnaire data revealed that 52.4% of volunteers use tampons every period, and the majority of volunteers rated the tampons as 5 on a 1–5 Likert scale regarding their perceived comfort using tampons. All (100%) of volunteers were happy to provide a tampon as a sample for testing. The findings from this study show that tampons and LVSs were comparable when analysing the vaginal microbiome, with potential superiority of the tampon with regard to patient acceptability. Self-collection of vaginal secretions for gynaecological screening using tampons warrants further research as this could change the screening landscape, ensuring wider participation and increasing efficacy.