When my knees first began hurting I was worried I was going to be sidelined but I think my legs were just adjusting to the high impact of running. Listen to your body and go easy until your knees feel better, and if the pain persists, definitely see a doctor. You don't want to do serious damage to your knees.
I went and got fitted for proper trainners on Sunday and took the shoes I had been wearing with me to the shop. As soon as the shop assistant saw them he knew immediately they were the culprit to my knee pain - apparently they are much too firm for running. He was so helpful and gave me lots of advice I think I tried on about 7 different pairs of trainners and had a quick run on the treadmill on each of them. He analysed my gait - I have a slight over pronation so a firm neutral shoe fixed it for me. I went for my first run in my new trainners and was holding out such hope that they would be the answer to my knee pain prayers and I am happy to say they are! The pain wasn't totally gone there's still a slight niggle there but definitely nowhere near the pain I had last week. Fingers crossed I have solved my problem and now I can focus on my stamina and speed.
I would recommend everyone get properly fitted for trainners, mine weren't cheap but they will be worth it - and as my boyfriend pointed out - its only about a 4 month gym membership.
If your interested I can recommend Runners Need for anyone in the greater London area. I went to the Canary Wharf branch and the staff were super helpful!