Geomagnetically induced currents (GIC) could saturate a transformer core and result in transformer stray flux heating. Many such incidents have occurred during the March 1989 K-9 solar magnetic disturbance. Stray flux distribution within a transformer is complicated and involves many factors. A systematic three dimensional analysis of transformer flux distribution under GIC is proposed. Magnetic fields everywhere inside a transformer will be calculated. Stray flux patterns as well as eddy currents for different transformer designs, core configurations will be analyzed and compared. The objectives of this study are to reveal the fundamental transformer magnetization mechanism under the influence of GIC, to assess potential stray flux heating possibilities of geologically vulnerable transformer units. The research findings will help utilities to justify the needs for mitigation actions on high risk units. Manufacturers may use the research results to review their design strategies and introduce possible design considerations to reduce GIC effects in the future.