The cellular fingerprint, a novel in silico screening approach, was developed to identify new biologically active compounds in combination with structural fingerprints. To this end, high-throughput screening (HTS) data from the National Cancer Institute have been used. To validate this method, we have selected the proapoptotic, natural compound betulinic acid (BA). Because of its antiproliferative effect on a variety of cancer cell lines, the identification of novel BA analogs is of great interest. Novel analogs have been identified and validated in different apoptosis assays. In addition, the novel approach exhibited a strong correlation between structural similarity and biological activity, so that it offers enormous potential for the identification of novel biologically active compounds.