If you have a medical condition that requires you to travel with medication, you should have your physician write a letter describing your condition and prescription medications, along with a list of any generic names of the prescribed medication. You should leave your medications in their original containers.
You may want to check if your medication is considered a narcotic drug in Germany. A list of substances subject to special regulations can be found on the following website: http://www.bfarm.de/EN/FederalOpiumAgency/narcoticDrugs/_node.html. If your medication is on this list, you will have to fill out a special form, which can be found on the same page (direct link to the form: http://www.bfarm.de/EN/FederalOpiumAgency/narcoticDrugs/Ein-Ausfuhr/_node.html;jsessionid=D723BD64224612F39E64EA4428505143.1_cid340. This form has to be filled out by the doctor and signed/authorized by a public health authority. It should be presented at customs.
Please avoid bringing large amounts of non-prescription drugs with you.