A fingerprint was developed to evaluate ten genotypes of Andrographis paniculata (a herbal drug) collected from different geographical locations. The genotypes were assessed by HPLC and the chromatogram areas were used to construct fingerprints. Between the two fingerprints, vector of differences was defined. The scalar mean of the deviated vector was used for statistical analysis. By incorporating appropriate chemometric methods better differentiation of samples was achieved. This provides tools for extracting relevant chemical information from the obtained data. The developed method can be used as a quality control tool for rapid authentication, identity, assessment and selection of good quality natural drug from a wide variety of herbal samples.