New molecular approaches are being developed to detect endometrial cancer using minimally invasive sampling methods. This study aims to evaluate the acceptability of self-collected cervicovaginal samples among women with Lynch syndrome, a group at high risk for developing endometrial cancer. Participants collected cervicovaginal self-samples and answered an at-home acceptability questionnaire in a cross-sectional study. Self-samples from a subset of these women were analyzed for somatic mutations using next-generation sequencing (NGS), targeting a panel of 47 genes. A total of 61 (88.4%) out of 69 eligible women participated in the study. The overall self-sampling experience was rated good or very good (N = 55, 90.2%). Most of the women were confident about correctly sampling (N = 58, 95.1%), and most reported no or mild pain (N = 56, 91.8%). During self-sample collection, most women reported feeling calm and comfortable and experiencing safety, privacy, and normality. In a pilot study using a subset of 15 samples, five somatic variants were identified in four self-samples (4/15, 26.7%) in ACVR2A, ARID1A, APC, and KMT2D. During follow-up, three out of four women with variants detected in the self-sample underwent prophylactic hysterectomy at a median of 9.1 months, while one out of four developed endometrial cancer after 3.9 years since the collection of the sample. Self-sampling is well-accepted and well-tolerated in women with Lynch syndrome and could potentially reduce some barriers associated with gynaecological surveillance. Further research is needed to evaluate the feasibility of implementing cervicovaginal self-collection and the accuracy of molecular testing for gynaecological surveillance in women with Lynch syndrome.