The asymptomatic nature of and lack of effective early-stage diagnostic tools in CKD, predisposes individuals to the risk of end-stage CKD and related complications. Whole blood microRNAs (miRNAs) have the potential for CKD risk screening. We evaluated the expression profile of six novel whole blood miRNAs as well as their ability to predict prevalent CKD in individuals with hypertension and/or diabetes. We included 911 individuals with hypertension and/or diabetes, of which 18.8% had prevalent CKD. The miRNA expression was analyzed using quantitative reverse transcription PCR (RT-PCR). Five of the six miRNAs, namely hsa-miR-novel-chr1_36178, hsa-miR-novel-chr2_55842, hsa-miR-novel-chr7_76196, hsa-miR-novel-chr5_67265, and hsa-miR-novel-chr13_13519, were significantly increased in people with CKD (all p < 0.028). Only the increased expression of hsa-miR-novel-chr2_55842 and hsa-miR-novel-chr7_76196 were independently associated with reduced estimated glomerular filtration rate (eGFR) (both p ≤ 0.038), while all the analyzed miRNAs were positively associated with prevalent CKD (all p ≤ 0.038). All the blood miRNAs were acceptable predictors of CKD (C-statistic > 0.7 for all), with similar predictive capacity (p = 0.202). However, hsa-miR-novel-chr13_13519 added to CKD prediction beyond conventional factors (p = 0.040). Novel whole blood miRNAs showed an acceptable discriminative power to predict prevalent CKD; thereby suggesting the potential use of these miRNAs, particularly hsa-miR-novel-chr13_13519, in clinical practice as a screening tool for CKD in high-risk individuals.