To date, there have been no large-scale national studies of the prevalence of chronic kidney disease in Kazakhstan. It includes the research based on the analysis of the estimated glomerular filtration rate (eGFR). The aim of this study was to investigate the population prevalence of CKD and associated risk factors in Kazakhstan. The cross-sectional study consisted of a nationally representative sample of n = 6 720 adults aged 18 to 69 from 14 regions and 3 major cities in Kazakhstan. The study covered the period from October 2021 to May 2022. The WHO STEPS questionnaire was used for the survey. For the diagnosis of CKD, creatinine levels in collected blood samples were measured to assess eGFR. Demographic characteristics were collected and studied. The total and adjusted prevalence of factors associated with the presence of CKD were calculated and analysed using logistic regression. 73.5% (n = 4940) of participants had normal eGFR, while 25.2% (n = 1695) had mild CKD (eGFR = 60–89 mL/min/1.7 m2). The overall prevalence of CKD with eGFR < 60 ml/min/1.7 m2 was 1.3% (n = 85), of which 0.2% (n = 15) had eGFR < 45 ml/min/1.7 m2. A mild degree of CKD was most often determined in residents of the East Kazakhstan region in 10.4%, and in 7.8–8.0% of cases. The majority of CKD patients was detected in the East Kazakhstan region and Almaty city, 15.3% and 10.6% of cases respectively. In mild and CKD with GFR < 60 ml/min/1.7 m2, the age of participants was 50–69 years in 61.5% and 78.8% of cases, respectively (p < 0.001). In addition to the association with the place of residence, a statistically significant relationship was found between the risk of developing CKD and underweight (OR 1.43, 95% CI (1.09–1.88), p < 0.001), as well as the presence of obesity (OR 1.24, 95% CI (0.99–1.53), p = 0.04). We observed the prevalence of CKD with eGFR < 60 ml/min/1.7 m2 at the level of 1.3%. However, a fairly large part of study participants had a mild CKD (25.2%). The results of this study can be used for the optimization of the doctors workload and the timely provision of care to patients with CKD.