Adoptive cell transfer is an important approach for basic research and emerges as an effective treatment for various diseases， including infections and blood cancers. Direct genetic manipulation of primary immune cells opens up unprecedented research opportunities and could be applied to enhance cellular therapeutic products. In this article， we report highly efficient genome engineering in primary murine T cells using a plasmid-based RNA-guided CRISPR system. We developed a straightforward approach to ablate genes in up to 90% of cells and to introduce precisely targeted single nucleotide polymorphisms in up to 25% of the transfected primary T cells. We used gene editing-mediated allele switching to quantify homology-directed repair， systematically optimize experimental parameters， and map a native B cell epitope in primary T cells. Allele switching of a surrogate cell surface marker can be used to enrich cells， with successful simultaneous editing of a second gene of interest. Finally， we applied the approach to correct two disease-causing mutations in the gene. Repairing the cause of the scurfy syndrome， a 2-bp insertion in and repairing the clinically relevant Foxp3 mutation restored Foxp3 expression in primary T cells.