Bed time routine. Does the toddler have a regular bed time routine? Does he fall asleep in his bed? Establish a regular bedtime routine, which may include a bath, reading a book, and falling asleep in his bed without a bottle or sippy cup. Toddlers and babies do best by falling asleep where they will be sleeping otherwise this can have them wake often. Consider teething, molars may be coming in, try motrin.
Avoid reinforcing. How do you respond when he awakens? Is there anything about waking at 3am that is good? Do you feed him, take him to your bed? Those might reinforce waking in the middle of the night. I need more information about how you put him to sleep for naps and bedtime. Record all sleeptimes, environment, routine as well as your response to awakening and visit your doctor for specific advice.