Monocytic cells unlike CD4+ T cells survive HIV induced apoptosis and serve as key viral reservoirs. Mechanisms underlying the development of resistance to HIV-induced cytopathic effects are poorly understood. In chronic HIV infections, microbial products translocate from the gut and may activate lymphocytes conferring anti-apoptotic signals. By using Vpr52-96 peptide, an accessory protein of HIV known to cause apoptosis in various cell types, as a model for apoptosis-inducing protein, we demonstrate that Vpr52-96 induced apoptosis in primary monocytes and undifferentiated THP-1 cells. However, monocyte-derived macrophages and PMA-differentiated THP-1 cells exhibited profound resistance to Vpr-induced apoptosis. Interestingly, prior treatment of primary monocytes and undifferentiated THP-1 cells with TLR-9 agonist, CpG, induced resistance to Vpr-mediated apoptosis. This resistance was found to be mediated by extracellular calcium influx, activation of c-Jun N terminal kinase via Calmodulin-dependent kinase II and induction of anti apoptotic cIAP2 gene. Our results also revealed a novel pathway by which Vpr may dysregulate TLR signaling in monocytes by targeting MyD88. Interestingly, CpG protected these cells by blocking the Vpr-induced inhibition of MyD88. Overall, our results suggest that anti-apoptotic cIAP2 gene and calcium activated JNK signaling play a crucial role in conferring resistance induced by CpG against Vpr-mediated apoptosis in monocytic cells.