Recently, we have shown that exposure of fetal thymus organ cultures (FTOC) to modeled microgravity (MMG) using a clinostat with a microgravity organ culture dish system (MOCDS) blocks T cell development in a manner independent of steroid stress hormones present in vivo. In this study, we describe the development of the MOCDS system, as well as its use in attempting to understand the mechanism by which T cell development is inhibited in MMG. We show that after MMG exposure FTOC exhibited a significant reduction in CD4+CD8+ double positive (DP) cell production, but those DP cells which remained expressed higher levels of the T cell receptor (TCR) associated molecule, CD3. Interestingly, CD4-CD8- double negative (DN) cells expressed lower levels of CD3 on their surface. DN, as well as immature single positive (ISP) cells, also expressed reduced levels of the IL-7 receptor alpha chain (CD127). These changes in CD3 and CD127 expression were concomitantly associated with an increased production of tumor necrosis factor (TNF)-alpha. We were also able to show that addition of an exogenous signal (anti-CD3epsilon monoclonal antibody) to these cultures effectively mitigated the MMG-induced effects, suggesting that MMG-exposure causes a signal dampening effect on developing thymocytes.