Purpose: Hypertension (HT), dyslipidemia (DL), and diabetes mellitus (DM) are major risk factors for cardiovascular diseases. Despite the wide availability of medications to reduce this risk, poor adherence to medications remains an issue. The aim of this study is to evaluate medication adherence of prevalent users in these disease medications (HT, DL, DM) using claims data. Factors associated with non-adherence were also examined. Methods: Of 7,538 participants of the Tsuruoka Metabolomics Cohort Study, 3,737（HT: 2,724, DL: 2,137, DM: 665) were identified as prevalent users of these disease medications. Information on lifestyle was collected through a questionnaire. Adherence was assessed by a proportion of days covered (PDC) and participants with PDC ≥ 0.8 were defined as adherent. Predictors of non-adherence were determined by performing multivariable logistic regression. Results: Medication adherence differed by medication groups. Those with DL-only showed the lowest adherence (79.6%), followed by those with DM-only (81.7%) and those with HT-only (89.8%). The associations were observed especially among those with no comorbidities. Determinants associated with non-adherence in each medication group were skipping breakfast and poor understanding of medications among those with HT, females, having comorbidities, having the medical history of stroke, and drinking habit among those with DL, and skipping breakfast among those with DM. Conclusion: While participants showed high medication adherence, differences were observed across medication groups. The identified predictors of non-adherence could help target those in need of adherence support.