Here we describe a morpholino-based gene knockdown microinjection protocol to interrogate gene function at the maternal-embryonic transition. We use morpholinos, which are chemically synthesized probes that specifically modulate gene expression, to study early mouse embryogenesis. This gene knockdown method works irrespective of the maternal or embryonic origin of gene expression and is independent of the endogenous RNA interference machinery. This protocol details the methods we use to introduce a morpholino into a fertilized one-cell mouse embryo and to validate the success of knockdown of the gene of interest. The rapid action of morpholinos is especially well suited to study gene function during the maternal-embryonic transition in ways that are not easily addressed even by conditional knockout mouse models. Application of this method significantly improves access to the gene regulatory network that controls reprogramming in the early mouse embryo.