In vivo imaging of treatment responses at the molecular level could have a significant impact on the speed of drug discovery and ultimately lead to personalized medicine. Strong interest has been shown in developing quantitative fluorescence-based technologies with good molecular specificity and sensitivity for noninvasive 3D imaging through tissues and whole animals. We show herein that tumor response to chemotherapy can be accurately resolved by fluorescence molecular tomography (FMT) with a phosphatidylserinesensing fluorescent probe based on modified annexins. We observed at least a 10-fold increase of fluorochrome concentration in cyclophosphamide-sensitive tumors and a 7-fold increase of resistant tumors compared with control studies. FMT is an optical imaging technique developed to overcome limitations of commonly used planar illumination methods and demonstrates higher quantification accuracy validated by histology. It is further shown that a 3-fold variation in background absorption heterogeneity may yield 100% errors in planar imaging but only 20% error in FMT, thus confirming tomographic imaging as a preferred tool for quantitative investigations of fluorescent probes in tissues. Tomographic approaches are found essential for small-animal optical imaging and are potentially well suited for clinical drug development and monitoring. drug discovery ͉ quantification ͉ three-dimensional T he ability to noninvasively image molecular processes in vivo is an emerging reality with different reporter and detection approaches (1, 2). Molecular imaging has been heralded to lead to earlier detection than current anatomical imaging approaches, which typically detect late-stage abnormalities. Another important prospect of molecular imaging is the ability to examine and quantify treatment responses in vivo by monitoring specific primary molecules or downstream targets. Therapeutic efficacy could then be probed dynamically on timescales of hours to days. This ability is in contrast to the mainstay of today's healthcare with traditionally late end points of drug efficacy, a practice that often impairs prompt revision and exclusion of ineffective treatment strategies with potentially lethal results.Drug-induced apoptosis is considered a generic biomarker of monitoring the effects of chemotherapeutic drugs (3), antihormonal therapeutics (4), or antiangiogenic therapies (5). Of several different detection methods, optical imaging is emerging as an important alternative to techniques using ionizing radiation and offers the advantages of stable fluorochromes, easier to perform chemistries, and portable and cost-effective imaging practices. Laxman et al. (6), for example, developed a recombinant luciferase reporter molecule that amplifies luminescence in apoptotic cells by specific cleavage of a Asp-Glu-Val-Asp fragment by caspase 3, which can be used in animal studies. Fluorescence detection using an annexin V probe tagged with a cyanine dye has been demonstrated by Schellenberger et al. (7) and Petrovsky et al. (8). Imagin...