When grown as 3D structures, tumor cells can acquire an additional multicellular resistance to apoptosis that may mimic the chemoresistance found in solid tumors. We developed a multicellular spheroid model of malignant mesothelioma to investigate molecular mechanisms of acquired apoptotic resistance. We found that mesothelioma cell lines, when grown as multicellular spheroids, acquired resistance to a variety of apoptotic stimuli, including combinations of TRAIL, ribotoxic stressors, histone deacetylase and proteasome inhibitors, that were highly effective against mesothelioma cells when grown as monolayers. Inhibitors of the PI3K/Akt/mTOR pathway, particularly rapamycin, blocked much of the acquired resistance of the spheroids, suggesting a key role for mTOR. Knockdown by siRNA of S6K, a major downstream target of mTOR, reproduced the effect of rapamycin, thereby confirming the role of mTOR and of S6K in the acquired resistance of 3D spheroids. Rapamycin or S6K knockdown increased TRAIL-induced caspase 8 cleavage in spheroids, suggesting initially that mTOR inhibited apoptosis by actions at the death receptor pathway; however, isolation of the apoptotic pathways by means of Bid knockdown ablated this effect showing that mTOR actually controls a step distal to Bid, probably at the level of the mitochondria. In sum, mTOR and S6K contribute to the apoptotic resistance of mesothelioma cells in 3D, not in 2D, cultures. The 3D model may reflect a more clinically relevant in vitro setting in which mTOR exhibits anti-apoptotic properties.