It is as the other person pointed out - your using muscles that you haven't been using on regular basis.
Try doing different exercises - or not do the same ones every time. If you are riding a bike - switch off to walking - that sort of approach.
Till your body gets used to it - you are going to have some discomfort.
becuase you are using muscles you havent used for a while
I think you need to back off for a bit. One of the classic mistakes is to start off too hard, seriously upset a lot of muscles that haven't had to do much in a long time, have some fairly severe pain up to and including spasming, and quit.
Instead, ease into it. Walk on the treadmill 20 minutes a day five days per week for awhile, and just get those muscles used to working again. gradually increase the rigor of your work out will your doing what you really want to be doing, but even then a maximum of 4 days a week for the really hard workouts and do an easy work out three days a week,,, just cardio or something like that.
If you are running, make sure you have good sneakers with the right support. Mainly, like everyone else said, stretching will help and breaking in the unused muscles. I would add some crunches, sit ups, some kind of core work too, (even 10 minutes before or after). It will make sure your posture and form are strong while doing the cardio and take un-needed pressure of the parts that do't need it.
Good job on the cardio! ;)
I have to do back strengthening exercises on a regular basis, to keep from getting backaches after doing cardio. I include sit-up, and one I call the booty lift. it's simple , you lay on the floor , on your back, knees bent, feet to the floor...and lift . do at least 3 reps of 10. also, take calcium magnesium pills . that's what works for me.
Is it a muscle pain or a skeletal pain? You should be stretching before you work out, and make sure not to lift weights the wrong way, and you shouldn't start off doing too much until you're ready for it.