Urinary N-acetyl-β-D-glucosaminidase (NAG) is an early marker for kidney injury. To explore the utility of urinary NAG in assessing kidney damage associated with metabolic syndrome (MetS), we investigated associations between urinary NAG levels and MetS factors. The study included 95 healthy controls, 51 hypertension (HTN) outpatients, 96 with type 2 diabetes mellitus (DM), and 80 with comorbidity of HTN and DM. We measured the NAG/creatinine (Cr), albumin/Cr, and protein/Cr ratios in urine, and collected data for MetS factors from the medical records. The urinary NAG/Cr ratio showed a significant increase in the HTN and DM groups than in the control (3.8, 3.6, and 2.8 IU/g·Cr, respectively). The urinary NAG/Cr ratio was significantly higher in normoalbuminuric DM patients (3.8 IU/g·Cr) than in the control (2.8 IU/g·Cr). Among MetS factors, high blood pressure, high fasting blood glucose, and low HDL-cholesterol were associated with high urinary NAG/Cr ratio in study subjects. Moreover, the subjects with 3 or 4 factors exhibited a higher urinary NAG/Cr ratio than those with less than 3 factors (7.4 vs. 3.3 IU/g·Cr). These results suggest that the urinary NAG/Cr ratio is a sensitive indicator for early injury of the kidney in association with MetS including DM.