BACKGROUND: Guidelines exist for chronic kidney disease (CKD) but are not well implemented in clinical practice. We evaluated the impact of a guideline-based clinical decision support system (CDSS) on laboratory monitoring and achievement of laboratory targets in stage 3-4 CKD patients. METHODS: We performed a matched cohort study of 12,353 stage 3-4 CKD patients whose physicians opted to receive an automated guideline-based CDSS with CKD-related lab results, and 42,996 matched controls whose physicians did not receive the CDSS. Physicians were from US community-based physician practices utilizing a large, commercial laboratory (LabCorp®). We compared the percentage of laboratory tests obtained within guideline-recommended intervals and the percentage of results within guideline target ranges between CDSS and non-CDSS patients. Laboratory tests analyzed included estimated glomerular filtration rate, plasma parathyroid hormone, serum calcium, phosphorus, 25-hydroxy vitamin D (25-D), total carbon dioxide, transferrin saturation (TSAT), LDL cholesterol (LDL-C), blood hemoglobin, and urine protein measurements. RESULTS: Physicians who used the CDSS ordered all CKD-relevant testing more in accord with guidelines than those who did not use the system. Odds ratios favoring CDSS ranged from 1.29 (TSAT) to 1.88 (serum phosphorus) [CI, 1.20 to 2.01], p < 0.001 for all tests. The CDSS impact was greater for primary care physicians versus nephrologists. CDSS physicians met guideline targets for LDL-C and 25-D more often, but hemoglobin targets less often, than non-CDSS physicians. Use of CDSS did not impact guideline target achievement for the remaining tests. CONCLUSIONS: Use of an automated laboratory-based CDSS may improve physician adherence to guidelines with respect to timely monitoring of CKD.