Tissue organogenesis is directed by both intercellular interactions and communication with the surrounding microenvironment. When cells are cultured on two-dimensional plastic substrata (2D), important signals controlling programs of cell proliferation, metabolism, differentiation and death responsible for the formation of correct tissue-specific architecture and function are lost. Designing three-dimensional (3D), physiologically relevant culture models, we can recapitulate some crucial aspects of the dynamic and reciprocal signaling necessary for establishing and maintaining tissue specific morphogenic programs. Here we briefly describe the details of robust methods for culturing mouse primary mammary organoids in 3D gels of different extracellular matrices and describe techniques for analyzing the resulting structures. These designer microenvironments are useful for both understanding branching morphogenesis and signaling integrations, but also for analysis of individual susceptibilities and drug testing.