Primary Muscles Used While Running. Primary muscles will get the most impact from your movement and therefore should receive more care. Your primary muscles while running will include your quads (quadriceps femoris), hamstrings, gluteus maximus, iliopsoas, and your calf muscles. quads. Your quads are muscle groups of four basic muscles located on your front thighs. You will be able to see and identify these muscles on the picture to your right.