Abstract: Objective To analyzed the genetic background of Atp11c gene trap mice. Methods The entire region PCR, was applied to find the gene trap vector insertion site and the lack state of the host chromosome.The fluorescent competitive PCR technology was used to detect the copy numbers of the integrated vector(s). Results The PCR results by 54 pairs of primers showed the trapping vector insertion site was in the first intron of,Atp11c gene, and the DNA sequencing results displayed 418 bp deletion on the host chromosome and more than 200bp missing on both ends of the vector. Fluorescent competitive PCR confirmed a single copy trapping vector inserted.Conclusion The genetic background of Atp11c gene trap have been resolved successfully and a program has been established to detect the genetic background of gene trap mice accurately and quickly.