One of the challenges for modern neuroscience is to understand the role of specific genes in the determination of cellular fate, and in the formation and physiology of neuronal-circuits. Techniques for genetic manipulation in vivo such as in utero electroporation are fundamental tools to address these issues. Here, we describe an established protocol for in utero electroporation in mouse and rat for reliable targeting of the hippocampus, the motor, prefrontal, and visual cortices, and the Purkinje cells of the cerebellum. The method is based on an electroporation configuration entailing commonly used forceps-type electrodes plus an additional third electrode. This configuration allows highly consistent direction of the electric field to the different neurogenic areas by simple and reliable adjustment of relative positions, polarities and/or dimensions of the electrodes. More than 70% of electroporated embryos survive to postnatal ages and around 60-90% express the electroporated vector, depending on the targeted area. By a single electroporation episode, the protocol enables for symmetric transfection in both brain hemispheres. The procedure requires 4 hours of preparation on the first day and it lasts 1 hour, including a surgery time of 30 mins, on the second day.