Bilateral squats are frequently used exercises in rehabilitation and sport performance programs. Lower extremity muscle activation may change based on alignment during the performance of the exercise. PURPOSE: To compare lower extremity muscle activation patterns during different squat techniques. METHODS: 28 healthy, uninjured volunteers (19F, 9M, 21.5 ± 3 yrs, 170 ± 8.4cm, 65.7 ± 11.8kg). EMG electrodes were placed on the vastus lateralis, vastus medialis, rectus femoris, biceps femoris, and the gastrocnemius of the dominant leg. Participants completed 5 instructed squats while purposefully displacing the knee medially (malaligned) and 5 instructed squats with neutral alignment (control). Normalized EMG data (MVIC) were reduced to 100 points, and represented as percentage of squat cycle with 50% representing peak knee flexion and 0% and 99% representing knee extension. Muscle activation was averaged across 10% bins for the entire squat and compared using paired t-tests between malaligned and control squats. RESULTS: The malaligned squat resulted in significantly reduced vastus lateralis activity during the first and last 10% of the malaligned squat compared to the control squat (0.15 ± 0.1 vs. 0.18 ± 0.13, p = .049; 0.35 ± 0.26 vs. 0.42 ± 0.31, p = .003). The malaligned squat resulted in significantly reduced vastus medialis activity during the first and last 10% (0.12 ± 0.08 vs. 0.14 ± 0.1, p = .019; 0.26 ± 0.17 vs. 0.33 ± 0.18, p = .0002). Rectus femoris activity decreased at 0-9% (0.1 ± 0.06 vs. 0.13 ± 0.08, p = .02), 30-39% (0.58 ± 0.48 vs. 0.81 ± 0.44, p = .001), 40-49% (0.63 ± 0.5 vs. 0.84 ± 0.51, p = .001), and 90-99% (0.18 ± 0.1 vs. 0.23 ± 0.13, p = .004) during the malaligned squat. Gastrocnemius activity decreased during the malaligned squat at 0-9% (0.076 ± 0.05 vs. 0.095 ± 0.06, p = .004), 10-19% (0.071 ± 0.049 vs. 0.084 ± 0.065, p = .02), and 20-29% (0.09 ± 0.06 vs. 0.1 ± 0.079, p = .03), but increased at 50-59% (0.14 ± 0.12 vs. 0.1 ± 0.067, p = .03), 60-69% (0.12 ± 0.1 vs. 0.086 ± 0.05, p = .014), 80-89% (0.14 ± 0.1 vs. 0.11 ± 0.07, p = .05), and 90-99% (0.13 ± 0.09 vs. 0.1 ± 0.07, p = 0.05) compared to the control squat. CONCLUSION: We observed decreased quadriceps and gastrocnemius activation, during the descending phase and increased gastrocnemius activation during the ascending phase of a malaligned squat.