ObjectivesFluctuating estradiol (E2) levels seem to be associated with menopausal symptoms, though not all women suffer from these symptoms to the same extent despite experiencing these hormonal changes. This suggests underlying, interindividual mechanisms, such as single-nucleotide polymorphisms (SNPs) influencing estrogen receptors α and β, and the g-protein-coupled estrogen receptor (GPER). As research is scarce, we aimed to address this research gap by assessing genetic traits, E2 levels, and menopausal symptoms longitudinally. Study design129 perimenopausal women (aged 40–56 years) participated in the 13-month longitudinal Swiss Perimenopause Study. Main outcome measuresMenopausal symptoms were assessed fortnightly using the Menopause Rating Scale (MRS II). Salivary E2 levels were assessed 14 times over two non-consecutive months. Blood samples were collected using the dried blood spot (DBS) technique to analyze ESR1 rs2234693, ESR1 rs9340799, ESR2 rs1256049, ESR2 rs4906938, and GPER rs3808350. Group-based trajectory modeling was performed to identify interindividual trajectories of menopausal symptoms. Multinomial logistic regression models were employed to identify factors associated with these trajectories. ResultsFour distinct trajectory groups of menopausal symptoms were identified (increase, moderate, rebound, decrease). ER gene polymorphisms and E2 fluctuation were significantly associated with group membership. Furthermore, ER gene polymorphisms modulated the effect of E2 fluctuations on menopausal symptom trajectory. ConclusionsThis study illuminates the multifaceted factors contributing to the individuality of the perimenopausal experience. ER gene polymorphisms emerged as integral factors by modulating the effect of E2 fluctuations on menopausal symptom trajectory. This underscores the intricate interplay of genetic factors, E2 fluctuations, and menopausal symptoms during perimenopause.