I need to take antibiotics because of non-gonoccocal urethritis or prostatitis. I am worried it may affect my health long term. Will it?

Antibiotics are not going to have a long term negative effect on your health. Good grief do you think they'd be the mostly widely prescribed medication if they were dangerous?

Yes they can make things uncomfortable and some people do have strong reactions to them, some people get explosive diarrhea or get an upset stomach. If that happens stop taking the pill, call your Dr. and find out what he recommends. If you have any problems don't eat any heavy foods, after you're done with the medication eat some yogurt, drink some probiatic juice and you'll be back to normal in no time.

No it won't destroy your gut flora permanently. Lots of men have taken a strong antibiotic regimen for such infections. Takes strong doses and lots of them to knock down the infection. I did one for 30 days once, did not cause me any issues at all.

You'll be fine.

Not taking the antibiotics will ensure that you don't have any long term health. Your gut flora is negotiable. If you suffer ill effects at the end of your course of treatment, you can regrow your gut fauna by taking probiotics.

It will affect your own antibodies putting you at a higher risk of infections but where I live only the doctor can prescribe antibiotics and they would not give you one if not needed - I don't understand why you are taking them for 2 weeks because the normal treatment for urethritis is - Treatment options are doxycycline 100 mg x 2 for one week or azithromycin 1 gram single dose or 1,5 gram distributed in five days.

They won't destroy your gut flora permanently, but you can try to fight the interim effects -- which could include a yeast infection -- with probiotics.

First, clear this with your doctor. Also have him or her give you a prescription for an anti-fungal (with a refill) in case a yeast infection occurs. The other danger is a C.diff infection, so talk that over with your doctor, too.

Second, take a probiotic 1-2 hours after taking your antibiotics. Do NOT take them with the antibiotics, only 1-2 hours later. You'll have to be careful about keeping track of the schedule. I also suggest that you eat 2 cups of PLAIN yogurt with live cultures per day.

Again, discuss all this with your doctor. I'm surprised he or she didn't raise the issue with you. You may still develop problems, but you may manage to prevent them with these steps.