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Most balance assessment studies using inertial measurement units (IMUs) in smartphones use a body strap and assume the alignment of the smartphone with the anatomical axes. To replace the need for a body strap, we have used an anatomical alignment method that employs a calibration maneuver and Principal Component Analysis (PCA) so that the smartphone can be held by the user in a comfortable position. The objectives of this study were to determine if correlations existed between angular velocity scores derived from a handheld smartphone with PCA functional alignment vs. a smartphone placed in a strap with assumed alignment, and to analyze acceleration score differences across balance poses of increasing difficulty. The handheld and body strap smartphones exhibited moderately to strongly correlated angular velocity scores in the calibration maneuver (r = 0.487-0.983, p < 0.001). Additionally, the handheld smartphone with PCA functional calibration successfully detected significant variance between pose type scores for anteroposterior, mediolateral, and superoinferior acceleration data ( p < 0.001).