Aim We investigated the characteristics of elderly medical patients with white matter hyperintensities on magnetic resonance imaging. Methods A total of 213 patients (123 men and 90 women; mean age 74.8 years) reported their history of hypertension, diabetes, dyslipidemia, previous stroke, coronary heart disease and chronic kidney disease (CKD). All patients completed the Mini‐Mental State Examination and Geriatric Depression Scale. White matter hyperintensities were evaluated for the periventricular region, basal ganglia (BGH), deep white matter and infratentorial region, and brain atrophy was calculated as bicaudate ratios. Results Patients with cognitive impairment (Mini‐Mental State Examination score < 24) were significantly older (P = 0.001), had periventricular region hyperintensities (P = 0.029) and BGH (P = 0.0015), and showed atrophy (P < 0.0001). Logistic regression showed that cognitive impairment was predicted by stroke (OR 2.5, 95% CI 0.033–0.894, P = 0.036) and atrophy (OR 8.43, 95% CI 5.71–37.0, P = 0.0109). Multiple regressions showed that BGH was associated with CKD (β = 0.213; P = 0.003), and infratentorial region was associated with stroke (β = 0.157; P =0.035) and CKD (β = 0.172; P = 0.016). Periventricular region was associated with age (β = 0.2; P = 0.011) and Geriatric Depression Scale (β = 0.151; P = 0.037), and deep white matter hyperintensities with age (β = 0.189; P = 0.016). Conclusions Although cognitive impairment in elderly medical patients is associated with stroke and brain atrophy, white matter hyperintensities, especially BGH and infratentorial region, are associated with cognitive decline in relation to CKD. Geriatr Gerontol Int 2016; ••: ••–••.