Running burns a lot of calories compared to other forms of cardio such as swimming and cycling because you are carrying your entire body weight at each step. But it is exactly for this same reason that running can also have negative effects on your body.
Every time one of your feet hits the ground the impact sends a shock wave up your leg and into your spine. This is why marathon runners commonly develop knee and lower back problems. In order to minimize damage you need to obtain proper running shoes and perhaps ask your physician about orthopedic knee support straps. You should try to take deliberately long strides while running so that you land on your heels. The stride should then ‘roll’ from your heel to the ball of your foot where it is lifted off the ground again. This rolling motion will translate some of the vertical momentum into horizontal momentum – reducing the stress on the rest of the body. Also make sure you run with a straight back, your head up and your eyes fixed ahead of you. This way you will run as efficiently as possible and reduce the negative effects.
However, no matter how good your shoes and your technique are, you will never eliminate the impact felt at each stride to zero during running. This is why you might want to consider switching to the cross trainer. This is an effective simulation of a running motion, but with none of the impact stress. In addition, you are working your arms, which means you are targeting more muscle groups and burning more calories. You can also vary the motion on a cross trainer from a cross-country skiing stride to a stair-climbing stride. In summary, cross training will yield all the benefits of running, without any of the negative aspects.