I have a canker sore in the back of my throat. is this bad?

Well...it's not good: Important to know how long its been there and your history with them. If you get them frequently & they come and go and this is pretty normal for you, speak with your doctor about antiviral medications (could be a herpetic lesion instead). If the lesion has been there longer than 2 weeks or if this is abnormal for you, see a doctor (dentist, ent, or oral surgeon) immediately.

No: Its an ulceration in the throat area thats all. It possesses no more of a threat to your health than any other canker sore just in a very uncomfortable area.