A fingerprint analysis method was developed for Ginkgo biloba leaves and was successfully used for quality evaluation of related health foods by HPLC with electrospray ionization MS. Fifteen samples of G. biloba leaves, which were collected from 15 different locations in China, were analyzed and identified in this study. By both peak analysis and similarity analysis of the fingerprint chromatograms, variation of constituents was easily observed in the leaves from different sources. By comparison with batches of authentic leaves, the authenticity, and quality consistency of related health foods in different matrixes were effectively estimated. It is important to mention that studying a wide range of authentic leaves from various habitats made the quality evaluation of commercial products more convincing and reasonable. The fingerprint-based strategy of the developed method should provide improved QC of G. biloba leaves and products.