Premature battery drain, swelling and fires/explosions in lithium-ion batteries have caused wide-scale customer concerns, product recalls, and huge financial losses in a wide range of products including smartphones, laptops, e-cigarettes, hoverboards, cars, and commercial aircraft. Most of these problems are caused by defects which are difficult to detect using conventional nondestructive electrical methods and disassembly-based destructive analysis. This paper develops an effective computed tomography (CT)-based nondestructive approach to assess battery quality and identify manufacturing-induced defects and structural deformations in batteries. Several unique case studies from commercial e-cigarette and smartphone applications are presented to show where CT analysis methods work.