In a previous study, we reported a list of genes expressed differentially in primordial and primary follicles [Park et al, Fertil. Steril., 83, 410-418 (2005)]. An innovative experimental system is required to evaluate the functions of these genes in folliculogenesis, particularly primordial-primary follicle transition. In this study, ovarian tissues were dissociated, and isolated cells were transfected using small interfering RNAs (siRNAs) for disrupting a specific gene, followed by ovarian reconstruction via calcium alginate encapsulation. The effects of RNA interference (RNAi) on follicular development were evaluated by a histological observation of the reconstructed ovarian tissue. Interestingly, follicular formation and development showed differences between control and experimental groups. Thus, even though this system includes some problems that need to be solved, ovarian reconstruction following the modification of gene expression of individual ovarian component cells could lead the way to methods of studying molecular mechanisms of primordial-primary follicle transition.