Bioengineered dental tissues and whole teeth that exhibit features and properties of natural teeth can functionally surpass currently used artificial dental implants. However, no biologically based alternatives currently exist for clinical applications in dentistry. Here, we describe a newly established bioengineered tooth bud model for eventual applications in clinical dentistry. We also describe methods to fabricate and analyze bioengineered tooth tissues, including cell isolation, in vivo implantation, and post-harvest analyses.