The global prevalence of chronic kidney disease (CKD) of uncertain etiology may be underreported. Community-level epidemiological studies are few due to the lack of national registries and poor focus on the reporting of non-communicable diseases. Here we describe the prevalence of proteinuric-CKD and disease characteristics of three rural populations in the North Central, Central, and Southern Provinces of Sri Lanka. Patients were selected using the random cluster sampling method and those older than 19 years of age were screened for persistent dipstick proteinuria. The prevalence of proteinuric-CKD in the Medawachchiya region (North Central) was 130 of 2600 patients, 68 of 709 patients in the Yatinuwara region (Central), and 66 of 2844 patients in the Hambantota region (Southern). The mean ages of these patients with CKD ranged from 44 to 52 years. Diabetes and long-standing hypertension were the main risk factors of CKD in the Yatinuwara and Hambantota regions. Age, exceeding 60 years, and farming were strongly associated with proteinuric-CKD in the Medawachchiya region; however, major risk factors were uncertain in 87% of these patients. Of these patients, 26 underwent renal biopsy; histology indicated tubulointerstitial disease. Thus, proteinuric-CKD of uncertain etiology is prevalent in the North Central Province of Sri Lanka. In contrast, known risk factors were associated with CKD in the Central and Southern Provinces.