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I just wanted to add, that I originally posted this exact same question back in December 2008 (Is it normal for my arm muscle in my shoulder to hurt 2 weeks after flu shot?, and my pain actually lasted for about 3-5 months.

I just got my flu shot this season (2009), and had no pain after flu shot...you can read about the experience (and how I spoke with the nurse about my previous bad experience; the needle was up too high...): NO PAIN in my arm or shoulder after flu shot this year!