Objectives: Exposure to cadmium (Cd) and mercury (Hg) is associated with renal dysfunction. This study aimed to determine the possibility of decreasing blood Cd and Hg levels in patients with chronic kidney disease (CKD).  Methods: Twenty-seven patients with CKD were enrolled in this prospective, single-arm pilot study. Patients with blood Cd levels ≥1.4 ug/L were instructed to decrease the intake of shellfish, while those with blood Hg levels ≥5.0 ug/L were asked to decrease the intake of external blue-colored fish. Results: Seven dialysis patients and 15 pre-dialysis patients completed the study. Compared with baseline, the blood Cd and Hg levels after 1 year were significantly decreased, although dietary intakes were not significantly different in patients with blood Cd levels ≥1.4 ug/L and blood Hg levels ≥5.0 ug/L. In pre-dialysis patients, the kidney function after 1 year worsened compared with that at baseline despite the reduction in blood Cd and Hg levels. Reduction of food intake containing Cd and Hg may lower the blood Cd and Hg levels in CKD patients with higher Cd and Hg levels.  Conclusions: Higher blood Cd levels may cause renal progression in pre-dialysis patients, and further studies are necessary to determine the cause.