In the past few years there has been an explosive growth in the development of chemically diverse libraries of molecules. Combinatorial libraries have proven to be a powerful method to examine structure-function relationships, and the synthesis and screening of small molecule libraries is emerging as an important strategy for drug discovery. 1 Several strategies have been employed to create and characterize these linear-and core-structured combinatorial libraries including: (i) solid phase and solution phase synthesis and (ii) grid, deconvolution, and tagging methods to identify compounds. 1 We describe herein the synthesis and characterization of directed combinatorial libraries of mesotetraphenylporphyrin (H 2 TPP) derivatives 3 -core-structured libraries-where the largest contains 1540 compounds (including isomers) (Figure 1). The derivitization of entire libraries to make them amphipathic (Figure 1) and the iterative selection of winning compounds by DNA binding are described. As a demonstration of the methodology, we find the dipositively charged porphyrins bearing at least one hydroxyl group to be the most efficacious in the photoinitiated cleavage of plasmid DNA.Both naturally occurring and synthetic porphyrins have long been known to exist in a large variety of isomers. For example, there are 60 possible isomers for protoporphyrin due to the four methyl, two vinyl, and two propionate groups on the eight pyrrole positions, and there are 420 possible isomers of the heme a prosthetic group in cytochrome a. 4 Similarly, we and others have exploited the six possible compounds and isomers when two different arylaldehydes are employed in the synthesis of meso-substituted porphyrins [5][6][7] and libraries of chemically inert, lipophilic, alkyl-substituted H 2 TPPs have been made. 8,9 The Photo *