This study characterizes the correlation between the chemical fingerprint and estrogenic activity of an Epimedium koreanum extract. The estrogenic activity of 31 E. koreanum extract samples was evaluated by a luciferase reporter gene assay, and the samples were classified into 3 groups based on their bioactivity. A chemical fingerprint analysis was performed on each sample by high-performance liquid chromatography (HPLC), and 44 common peaks were selected from the chromatogram and used as a dataset for a pattern recognition analysis. A canonical discriminant analysis performed on this dataset determined a distinct distribution of the samples according to their estrogenic activity on the scoring plot. The classification results showed that 90.3% of the original grouped cases had been correctly classified. The total content of the 4 major extract compounds, epimedin A, epimedin B, epimedin C, and icariin, exhibited good correlation (r=0.784) with the estrogenic activities of the respective extracts. This chromatographic fingerprint-chemometric analysis system could be useful for predicting the E. koreanum pharmacological activity and consequent biological activity-relevant quality control assessment.