Abstract We investigated inconsistencies between results for cystatin C (Cys C) and creatinine (Crea) in patients undergoing health check-ups. Data from 36,836 individuals who underwent health checkups at Huashan Hospital over the previous 3 years were analyzed. We extracted laboratory results of 10 biomarkers and information on sex and age. After applying detailed screening criteria, 14,968 participants were included in this study. We evaluated the consistency of the current reference intervals (RIs) for Cys C and Crea in assessing renal function across sex and age groups. The results showed that the current RIs led to inconsistent result interpretations when applied to different age and sex groups. Older individuals and men were more likely to have Cys C levels above the RIs whereas younger individuals were more likely to exceed the RIs for Crea. Age- and sex-dependency was observed for both biomarkers. We therefore developed new age- and sex-partitioned RIs for these markers. The updated RIs greatly improved the consistency of Cys C and Crea result interpretation across age and sex groups. Our findings indicated that Cys C and Crea are both dependent on age and sex, and using age- and sex-partitioned RIs improves interpretation consistency across different age and sex groups.