MicroRNAs (miRNAs) are noncoding RNAs that regulate post-transcriptional gene expression. In this study we characterized the circulating and urinary miRNA pattern associated with reduced glomerular filtration rate using Affymetrix GeneChip miR 4.0 in 28 patients with chronic kidney disease (CKD). Top miRNA discoveries from the human studies were validated in an Alb/TGF-β mouse model of CKD, and in rat renal proximal tubular cells (NRK52E) exposed to TGF-β1. Plasma and urinary levels of procollagen III N-terminal propeptide and collagen IV were elevated in patients with decreased estimated glomerular filtration rate (eGFR). Expression of 384 urinary and 266 circulatory miRNAs were significantly different between CKD patients with eGFR≥30 vs. <30 ml/min/1.73 m2. Pathway analysis mapped multiple miRNAs to TGF-β signaling-related mRNA targets. Specifically, Let-7a was significantly downregulated and miR-130a was significantly upregulated in urine of patients with eGFR<30; miR-1825 and miR-1281 were upregulated in both urine and plasma of patients with decreased eGFR; and miR-423 was significantly down regulated in plasma of patients with decreased eGFR. miRNA expression in urine and plasma of Alb/TGF-β mice generally resembled and confirmed most, although not all, of the observations from the human studies. In response to TGF-β1 exposure, rat renal proximal tubular cells overexpressed miR-1825 and down regulated miR-423. Thus, miRNA are associated with kidney fibrosis and specific urinary and plasma miRNA profile may have diagnostic and prognostic utility in CKD.