BACKGROUND: Chronic kidney disease (CKD) is an irreversible disease that diminishes length and quality of life. Emerging evidence suggests CKD progression and genomic integrity are inversely and causally related. To reduce health complications related to CKD progression, chronic aerobic exercise is often recommended. To date, appraisals of differing modes of exercise, along with postulations regarding the mechanisms responsible for observed effects, are lacking. In order to examine the ability of aerobic exercise to encourage improvements in genomic integrity, we evaluated the effects of 8 weeks of high-intensity interval training (HIIT; 85 % VO2max), low intensity training (LIT; 45-50 % VO2max), and sedentary behaviour (SED), in an animal model of early-stage CKD. METHODS: To assess genomic integrity, we examined kidney-specific messenger RNA (mRNA) expression of genes related to genomic repair and stability: Fan1, Mre11a, and telomere length as measured by T/S ratio. RESULTS: Following HIIT, mRNA expression of Fan1 was significantly up-regulated, compared to SED (p = 0.026) and T/S ratio was significantly increased, compared to SED (p < 0.001) and LIT (p = 0.002). CONCLUSIONS: Our results suggest that HIIT is superior to SED and LIT as HIIT beneficially influenced the expression of genes related to genomic integrity.