Background Cerebral microbleeds are an important radiologic marker of bleeding-prone brain and have been reported to be associated with the increased risk of intracerebral haemorrhage. Aims We sought to examine the association of chronic kidney disease with cerebral microbleeds, and determine whether the association differs between patients with and without diabetes. Methods A total of 909 patients with ischemic stroke who were consecutively admitted to our hospital were included in this study. We collected demographic, clinical, and laboratory data (including serum creatinine levels) and documented the presence and numbers of microbleeds. Kidney function was estimated by using the Modification of Diet in Renal Disease formula. We categorized estimated glomerular filtration rates into moderate to severe, mild, and normal (<60, 60–90, and >90 ml/min/1.73 m², respectively). Results Cerebral microbleeds is most frequent in the moderate-to-severe chronic kidney disease group (45.6%). In patients without diabetes, mild and moderate-to-severe chronic kidney disease was found to be independently associated with the presence of cerebral microbleeds (adjusted odds ratio, 1.68; 95% confidence interval, 1.04–2.71 and adjusted odds ratio, 3.74; 95% confidence interval, 1.87–7.47) compared with normal kidney function. In patients with diabetes, however, this relationship was not found. Furthermore, ordinal logistic regression analysis revealed that an increased serum creatinine level and a reduced kidney function were associated with the number of cerebral microbleeds. Conclusion We found that chronic kidney disease is independently associated with cerebral microbleeds in patients without diabetes but not in patients with diabetes.