In vitro developmental model systems have been an important tool for advancing basic research in the embryology and teratology fields. The rat and zebrafish embryo models have had broad utility in both fields for many decades. Furthermore embryonic stem cells, applied as a basic research tool, have broad applications across the development fields and many other fields including cancer, regeneration and epigenetic research. These models have historically been applied in mechanistic studies but were also considered promising for evaluating teratogenic potential of test substances. In recent years, in vitro teratogenicity assays have become an area of interest for supporting the 3 Rs (reduction, refinement, and replacement of animal use). Generation of such assays also provides a means to facilitate early assessment of test agents at a higher throughput without excessive use of animals. In this review, the three models are described with an emphasis of how they are being developed and/or refined to support teratogenicity assessment as screening tools. An overview of the state of the science and future directions are described. Birth Defects Research (Part C) 90:87–98, 2010. © 2010 Wiley-Liss, Inc.