Structure-activity relationship techniques were employed to classify fluoroquino- lones against S.pneumoniae. Density functional theory (DFT) was used to calculate a set of mo- lecular descriptors (properties) for eighteen fluoroquinolones. The descriptors were further analyzed using the principal component analysis (PCA), hierarchical cluster analysis (HCA) and K-nearest neighbor (KNN) chemometeric method. The PCA and HCA methods are quite efficient to classify the eighteen compounds into two groups (active and inactive) according to their degrees of anti- S.pneumoniae activity. The classified result is consistent with the clinic experimental result. The PCA shows that the variables Q3 (net charge on atom 3), QA (net charge on ring A), QB (net charge on ring B), VOL (molecular volume) and A (surface area) are found to be responsible for the sepa- ration between compounds with higher and lower anti-S.pneumoniae.