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Germination is a natural and efficient approach to improve nutrients and bioactive compounds of seeds through activation of dormant enzymes during sprouting. Nevertheless, over-sprouting may reduce the mixing strength of wheat flour, resulting in sticky dough and smaller loaf volume. Controlled germination could be a solution to improve the nutritional benefits while maintaining the end-use performance of whole-wheat flour (WWF). This study was undertaken to investigate the effect of germination time on WWF functionality. Three classes of U.S. wheat were used in the controlled germination process, including hard red spring (HRS), hard white (HW), and soft white (SW) wheat. After germinating from 5 to 24 hours, the sprouted wheat was dried (800C, 3 hours) for WWF milling and quality analysis. Falling number (FN), glucose and protein content were determined by sampling hourly from 5 to 15 hours of germination. The Mixolab test was performed to assess dough mixing and starch pasting properties of selected WWF with FN values in the ranges of 100-200, 200-300, 300-400, and 400-500 s. Wheat FN values before germination were 478 (HRS), 519 (HW), and 381 s (SW), but they decreased from 435 to 56, 482 to 65, and 345 to 57 s, respectively, during 5 to 24 hours of germination. The glucose content increased by 4-37% and 227-357%, respectively, after 5 and 15 hours of germination. Protein content was not significantly changed during 15 hours of germination. The Mixolab test showed that C1 (development time), stability time, and C2 (protein weakening during heating) increased, whereas C3 (pasting viscosity peak), C4 (pasting viscosity minimum torque), and C5 (retrogradation final torque) decreased after germination. This study indicated that the controlled germination process could improve the end-use performance of WWF in bread and other products.