Branching morphogenesis is a central process in renal development, but imaging and quantifying this process beyond early organogenesis presents challenges due to growth of the kidney preventing ready imaging of the complex structures. Current analysis of renal development relies heavily on explant organ culture and visualization by confocal microscopy, as a more developmentally advanced native tissue is too thick for conventional microscopic imaging. Cultured renal primordia lack vascularization and a supportive matrix for normal growth, resulting in tissue compression and distortion of ureteric branching. To overcome this, we used optical projection tomography to image and reconstruct the branching ureter epithelium of ex vivo embryonic kidneys and developed software to quantify these three-dimensional (3D) data. Ureteric branching was assessed by measuring tree and terminal branch length, tip number, branching iterations, branch angles, and inter-tip distances in 3D space. To validate this approach for analyzing genetic influences on renal development, we assessed branching and organ morphology in Tgfbeta2(+/-) embryos from E12.5 through E15.5. We found decreased branching, contrary to previous findings using organ culture, and quantified a primary defect in renal pelvic formation. Our approach offers many advantages from improved throughput, analysis, and observation of in vivo branching states, and has demonstrated its utility in studying the basis of renal developmental disease.