ABSTRACT: Successful spermatogenesis requires autocrine, paracrine, and endocrine signaling throughout the testes. The seminiferous tubules contain somatic Sertoli cells in tight association with numerous germ cell populations. To address the in vivo biologic roles of genes during spermatogenesis, spatial and temporal restriction of gene inhibition is a useful approach. To this end, Cre-LoxP technology can produce cell-specific knockdowns of genes, allowing dissection of the underlying processes that manifest as functional deficits in whole animals. Here we report the use of the synaptonemal complex protein 1-Cre (Sycp1-Cre) to create germ cell—specific nuclear factor κB knockdown mice through floxed IκB kinaseβ. We observed a LoxP gene recombination rate of approximately 43% using Sycp1-Cre, as determined by offspring genotype. In addition, we confirm that, with multiple generations, the LoxP sites fail to recombine due to epigenetic modification. This detailed examination of the meiotic Sycp1-Cre recombinase activity highlights the obstacles to germ cell—specific gene inhibition through Cre/LoxP technology in the testis. Taken together, these data demonstrate a need for early spermatogonial expression of Cre recombinase, as an alternative to meiotic Cre expression, for the creation of germ cell—specific knockout mice.