Background Cognitive impairment (CI) in chronic kidney disease (CKD) is highly prevalent and is associated with multiple limitations to the patients who show a higher mortality, more days of hospitalisation and a lower quality of life. Frailty in CKD is associated with adverse health outcomes and is also highly prevalent. The aim of our study was to determine the prevalence and characteristics of CI and relate the findings to frailty, mobility, muscle strength, and Health-Related Quality of Life (HRQoL). Methods Non-dialysis patients with CKD-Stages 3–5 were prospectively evaluated for inclusion. Excluded were patients with other cognitive disorders; signs of overt uremic encephalopathy; severe infection and hyponatremia. All patients underwent psychometric testing (5 different tests), assessment of mobility, strength, frailty and evaluation of HRQoL. Based on the number of pathological psychometric test results we established 2 different definitions of CI: subclinical uremic encephalopathy (SUE1: one pathological test; SUE2: two or more pathological test results). Results Sixty-two patients were included [median age 66 (IQR 57–75); male 55%]. Most patients had CKD-Stage 3 (3: 48%; 4: 32%; 5: 19%). CI was highly prevalent (SUE1: 60%; SUE2: 42%) and associated to a higher risk of falls (pathological Tandem-Gait-Test; SUE 1: 50% vs. 16%, P = 0.023; SUE2: 69% vs. 15%, P = 0.001), lower muscle strength (SUE 2-pathological: 39% vs. 7%, P = 0.008), frailty (SUE1: 59% vs. 28%, P = 0.038; SUE2: 67% vs. 33%, P = 0.028) and HRQoL. Conclusion CI is highly prevalent in non-dialysis CKD-patients. Even mild CI is associated with a decrease in mobility, muscle strength, HRQoL and frailty.