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We studied the thermal stability of new amorphous ZrAl-based magnetic tunnel junctions (MTJs) with a ZrAl-oxide barrier replacing the Ta layers traditionally used for the under and capping layers. The MTJs were compared with similar conventional MTJs (Ta-based MTJ with Al-oxide). After annealing at various temperatures up to 450°C, the ZrAl-based MTJs still had a significant tunnel magnetoresistance signal of nearly 21%. The thermal stability of amorphous ZrAl-based and conventional Ta-based MTJs differs dramatically, mainly because of the different microstructural evolution. The noncrystalline ZrAl-alloy film had superior surface uniformity and an induced microstructure that resisted interdiffusion, with dense, equiaxed grains making up the upper stacks' films. By contrast, the conventional Ta-based MTJ had a broad columnar structure with less dense boundaries, which act as a source of interdiffusion, resulting in barrier deformation at elevated temperatures.