The vaginal microbiome plays a major role in female and reproductive health. To understand the dynamics of the vaginal microbiome and the changes that occur leading to disease development in the vagina, it is important to define a normal, healthy vaginal microbiome to be used as baseline for research. The Vaginal Microbiome in Gynecological Health (VaMiGyn) is a metagenomic study on the vaginal microbiome of healthy Swedish women. Women were recruited by sending invitations by regular mail to all women invited to the organized cervical screening programme in Uppsala County, Sweden. Participating women donated a vaginal swab sample between September 2017 and February 2020 and answered an online questionnaire on socioeconomic, lifestyle and health questions.