Recently it has been reported that the estimated glomerular filtration rate (eGFR) is higher in habitual coffee consumers than in noncoffee consumers. However, the causality remains unclear. Therefore, we conducted a clinical trial to investigate the effects of coffee consumption on kidney function. Nineteen asymptomatic nonsmokers aged 21–27 years old participated in this study. They consumed coffee (18 g coffee beans/450mL per day) or green tea as a comparator for 2 weeks in a crossover design. Although creatinine-based eGFR was not affected after consuming either beverage, all cystatin-C-based eGFRs determined using five different equations were significantly increased after coffee consumption (means: 5.0–7.7%), but not after green tea consumption (means: 0.1–1.6%). Serum adiponectin andmagnesiumlevels increased significantly after coffee consumption (means: 13.6% and 4.3%, resp.), but not after green tea consumption. These findings suggest that even a short period of coffee consumption may increase cystatin-C-based eGFR, along with favorable changes in serum adiponectin, in healthy young adults.