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Objectives To date, no worldwide studies have been conducted to estimate the biological age of five organs using clinical biomarkers that are associated with the aging status. Therefore, we conducted this study to develop the models for estimating the biological age of five organs (heart, lung, liver, pancreas, and kidney) using clinical biomarkers which are commonly measured in clinical practice. Design A cross sectional study. Methods Subjects were recruited from the routine health check-up centers in Korea from 2004 through 2010. Data obtained from 121,189 subjects (66,168 men and 55,021 women) were used for clinical evaluation and statistical analysis. We examined the relations between clinical biomarkers associated with five organs and the chronological age and proposed a model for estimating the biological age of five organs. Results In the models for predicting the biological ages of the heart, lung, liver, pancreas and kidney in men, 12, 2, 8, 3, and 5 parameters were respectively included (R2 = 0.652, 0.427, 0.107, 0.245, and 0.651). In contrast to men, 10, 2, 8, 3, and 5 parameters in women were respectively included (R2 = 0.780, 0.435, 0.140, 0.384, and 0.501). Conclusion We first proposed the models for predicting the biological age of five organs in the current study. We developed those using clinical parameters that can be easily obtained in clinical practice settings. Our biological age prediction models may be used as supplementary tools to assess the aging status of five organs in clinical practice settings.