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Chronic kidney disease (CKD) is a debilitating systemic condition. Our working hypothesis is that CKD predialysis patients with periodontitis would respond poorly to periodontal treatment owing to immunologic compromise. Twenty-one predialysis patients (group 1) and 19 individuals without clinical evidence of kidney disease (group 2) with chronic periodontitis were subjected to non-surgical periodontal treatment with no antibiotics. Clinical periodontal and systemic parameters were evaluated at baseline and 3 months after treatment. Both groups showed significant and similar post-treatment improvements in all periodontal parameters examined. Most interestingly, periodontal treatment had a statistically significant positive effect on the glomerular filtration rate of each individual (group 1, p = 0.04; group 2, p = 0.002). Our results indicate that chronic periodontitis in predialysis kidney disease patients improved similarly in patients with chronic periodontitis and no history of CKD after receiving non-surgical periodontal therapy. This study demonstrates that CKD predialysis patients show a good response to non-surgical periodontal treatment.