Polypharmacy (PP) occurs in patients with type 2 diabetes (T2DM) owing to multimorbidity. We evaluated concomitant PP and medication adherence in T2DM 3 years after initiation of administration of a hypoglycaemic agent using a nationwide claim-based database in Japan. Factors associated with medication PP and imperfect adherence were identified using multivariable logistic regression. PP was defined as using ≥6 medications. Patients with proportion of days covered (PDC) of <80% were defined as having poor medication adherence. A total of 884 patients were analysed. Multivariate analysis revealed that age, total number of consultations and body mass index (BMI) are factors that influence PP. Factors associated with PDC < 80% were 2-3, 4-5 and ≥ 6 medications compared with 1 medication, male sex, <17 consultations and age 50-59 and ≥ 60 years compared with <40 years. In conclusion, older age, high total number of consultations and BMI ≥ 25 kg/m2 are risk factors for PP. PP influenced good medication adherence at the end of the observation period.