RNA interference (RNAi) has recently emerged as an efficient method to silence gene expression in mammalian cells by transfection of small interfering RNAs (siRNAs). The Janus kinase 3 (JAK3) is also pertinent to the development of a new immuno-suppressant. This study aimed to inhibit JAK3 expression using RNAi to determine allograft tolerance. To silence JAK3 expression, one dsRNA was tested to incorporate the JAK3 mRNA sequence. The expression vector containing the pre-mRNA expression cassette was transfected into rat basophilic leukemia cell line, RBL-2H3, for RNAi analysis (in vitro). The alloskin and composite tissue allograft were then transplanted to recipients using RNAi protocol to determine the allograft tolerance (in vivo). The results showed effective in vitro and in vivo downregulation of JAK3 expression by RNAi. Moreover, the histology of alloskin graft and composite tissue allograft (in vivo) under the siRNA showed more prominently diminished inflammatory infiltration than the control group. This is the first time in the literature that the suppressive effect of JAK3 silenced by siRNA has been tested both in vitro and in vivo, and shows that siRNA is capable of specific and functional silencing in allograft rejection.