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The dependence of dynamic random access memory (DRAM) device performance on trench and stack cell structures was first observed by changing the process position of passivation annealing. For the trench DRAM, the data retention fail bit counts (FBCs) decreased by 18% and the cell transistor threshold voltage (CTVth) shift by 53 mV. The FBCs are primarily influenced by the junction leakage current. In contrast, for the stack DRAM, the data retention FBCs increased by 225% and the CTVth shift increased by 20 mV. The FBCs are primarily influenced by the gate-induced drain leakage (GIDL) current because of the large gate and the drain overlap region in the recess channel array transistor (RCAT). The interface states increased after the deposition of the plasma nitride layer, as observed in the charge pumping measurement in the trench DRAM. Transmission electron microscopy indicated that the gate oxide thickness in the bottom region of the RCAT is thinner to generate gate oxide leakage. Furthermore, a decrease in the activation energy from 0.64 to 0.55 eV implies the occurrence of GIDL current, which corresponds to the FBC analysis result. This paper demonstrated that the passivation annealing position requires careful adjustment for device and manufacturing optimization.