As a biped, humans are designed to run in an upright position. People first ran for survival and hunting but now your running is more likely to be for pleasure. Running is primarily an aerobic activity although faster running and sprinting is anaerobic. When you run, you use a variety of muscles all of which may undergo hypertrophy, or growth. Even if your leg muscles do not bulk up as a result of your running, you will increase their strength, tone and endurance.
Ankle Extension and Flexion
As you push off of the ground, your ankle extends, correctly termed plantar flexion, which works the gastrocnemius and soleus muscles of your calf. These two muscles are connected to your heel bone via your Achilles tendon. As your foot returns to the ground ready for the next step, you must pull your toes up into dorsi flexion which works the muscles located on the front of your shin--the tibialis anterior.
Knee Flexion and Extension
Pulling your leg up behind you to drive yourself forward works your hamstrings. Your hamstrings are located on the back of your thigh and work along with the muscles of your hip to power you along the ground. Your quadriceps, at the front of your thigh, extends your knee to take the next step and absorb the impact of your landing and get a good workout as you run.
Hip Extension and Flexion
Extending your leg behind you to push you forward develops your gluteus maximus. The glutes, along with the hamstrings, contract to extend your hip. The greater your degree of hip extension, the more work is performed by your glutes and hamstrings--sprinting will build these muscles more than jogging. When you swing your leg forward to take another step you use your hip flexors at the front of your hip and your rectus femoris, one of the quadriceps muscles.
The muscles of your inner and outer thigh--your adductors and abductors--get a good workout while you run. Their role is to stabilize your hips and stop your knees from dropping inward or outward. These muscles are working isometrically--they are producing force but not actually moving.
The muscles of your core--the rectus abdominus, obliques, erector spinea and transverse abdominus--all work together to keep your spine aligned as you run. Running gives your core muscles an effective workout through the consistent spinal rotation that occurs when your arms and legs come forward with each stride. Running on terrain and uneven surfaces also challenges your core as you work maintain your balance and stability.
Shoulder Flexion and Extension
Most of the upper body movement in running comes from your shoulders. Swinging your shoulders forward uses your anterior deltoid which is your front shoulder muscle. Extending your arm backward is the job of your latisimus dorsi muscle of your back and your posterior deltoid. There is very little work being done by your upper body muscles in distance running so any building effect will be very slight. You use your upper body muscles far more in sprinting.