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Background Chronic kidney disease (CKD) is an important public health problem. Most of the evidence on its costs relates to patients receiving dialysis or kidney transplants, which shows that, in these phases, CKD poses a high burden to payers. Less evidence is available on the costs of the predialytic phase. Objective The aim of this study was to estimate the annual cost of patients with CKD not receiving dialysis treatment, using the Italian healthcare system perspective and a prospective approach. Methods A 3-year observational study (December 2010–September 2014) was carried out to collect data on resource consumption for 864 patients with CKD. Costs were estimated for both patients who completed the follow-up and dropouts. Results The mean annual total (healthcare) cost per patient equalled €2723 (95% confidence interval 2463.0–2983.3). Disease severity (higher CKD stage), multiple comorbidities, dropout status and belonging to the southern region are predictive of higher costs. Pharmaceuticals, hospitalisation, and outpatient services account for 71.5, 18.8 and 9.7% of total healthcare expenditure, respectively. Recent estimates of Italian costs of patients receiving dialysis are nine times the unit costs of CKD for patients estimated in this study. Unit costs at stage 5 CKD (the highest level of severity) equals 4.7 times the costs for patients at stage 1 CKD. Conclusion Despite its limitations, this study provides further evidence on the opportunity to invest in the first phases of CKD to avoid progression and an increase in healthcare costs.