Historically, the German language underwent two major sound shifts (Grimm's law and High German consonant shift, a.k.a. "Erste Lautverschiebung" / "Zweite Lautverschiebung"). However, neither sound shift encompassed the whole "Sprachraum" (language area), effectively dividing German accents into three major areas, depending on which of the sound shifts affected them and which didn't. Add the numerous regional dialects, and the German language is a versatile one indeed.
There are variations in pronunciation as well as in vocabulary ("Kolter" for a blanket in Hessen, but they know to call it "Decke" when talking to a non-native; "Pölter" for pyjamas in Ostwestfalen which they would call "Schlafanzug" when talking to someone from abroad, like someone from Cologne... ;-) ). The regional vocabulary is not likely to show up in standard learning material, and the pronunciation differences are not so bad as to really impede communication. (While an Australian sounds funny to an American, and uses a couple of strange words, you still understand each other without major difficulties. It's the same for a Frisian and an Austrian. The occasional misunderstanding is taken in stride and with a smile.)
Bottom line, accents differ significantly, but I wouldn't worry about it.