The chemotherapy sensitive Lewis lung carcinoma (LLC) and chemotherapy resistant Lewis lung carcinoma (CR-LLC) tumors concurrently implanted in mice, and compare these findings with histological macroscopic observations against 3D reconstruction of Fluorescence Molecular Tomography (FMT) preformed in vivo on the same animals. For the 3D image reconstruction we used 32 laser source images, a flat image and 3D surface rendering that confused for 3D Fluorescence Molecular Imaging (FMI). A minimum of ten tissue sections were analyzed per tumor for quantification of the TUNEL-positive cells, cell-associated Cy5.5-Annexin and vessel-associated Alexa Fluor-Lectin. These are useful apoptosis and angiogenesis markers, and they serve as validation experiments to data obtained in vivousing a Cy5.5-Annexin V conjugate injected intravenously in chemotherapy-treated animals carrying the tumors studied histologically. We detected higher levels of apoptosis and corresponding higher levels of Cy5.5 fluorescence in the LLC vs. the CR-LLC tumors according to tissue depth and these findings confirm that in vivo staining with the Cy5.5-Annexing conjugate correlates well with in vitro TUNEL staining and is consistent with the higher apoptotic index expected from the LLC line. There appeared to be 1.38% more apoptosis for LLC than CR-LLC. Consequently there is good correlation between the histology results and in vivo fluorescence-mediated optical imaging. In conclusion the apoptotic images of 3D FMI were validated by microscopic histological image analysis. This is a significant result for the continuous progress of fluorescence 3D imaging research.