A novel method of double qualitative similarities and double quantitative similarities was established for the evaluation of chromatographic fingerprints and it has been applied on the quality assessment of the high performance liquid chromatographic (HPLC) fingerprint of ginkgo leaf extract and dipyridamole injection. The chromatographic fingerprints containing 41 co-possessing peaks were obtained by choosing rutin peak as the referential peak. The chromatographic fingerprints were evaluated by the double qualitative similarity parameters (S and S') and the double quantitative similarity parameters (C and P). A variety of characteristics were investigated when big peaks and small peaks were missing. S can clearly reflect the distribution of chemical constituents, and C can reflect the total content of the co-possessing peaks of the sample, but both of them were significantly influenced by the big peaks and not by the missing of small peaks. S' and P are of equally weighing to all fingerprint peaks, and they can reflect sensitively the missing of small peaks . The double qualitative similarities (S and S') and the double quantitative similarities (C and P) can be combined to provide accurate qualitative and quantitative assessments for the quality of traditional Chinese medicine with regarding to the changes or lacks of both big peaks and small peaks. Meanwhile, the concepts of direction cosine and decomposition value of similarity were firstly put forward to describe the characteristics of chromatographic fingerprints, by which the contribution of each common peak to total similarity and the change of similarity under the missing of different peaks were quantified. The HPLC fingerprints can be used in the quality control of ginkgo leaf extract and dipyridamole injection.