M.M.
Hi A.!
Your poor little guy!!
If the test comes back negative, I would ask for another test. I haven't had this experience myself, but I know two moms whose daughters were initially diagnosed with negative cultures, but the doctors did a more thorough test and they DID find a bladder infection after all.
If your doctor says no to the second (I believe more extensive?) test, then take him to another doctor who is willing to look at this more carefully.
Finally, is his private part (don't want to write the word or this email could be deleted!) red or irritated? Is it possible there is a tear or cut on the outside?
My daughter was playing at a park when she was about 2 years old and she fell down in some bark and branches. She cried initially and then cried off and on for about a week, particularly when she peed. When I was finally able to get a good luck down there (much harder to do with a girl!), I saw she had a small cut. Urine is acidic and it was no doubt stinging her everytime she peed. Once the cut healed, she stopped complaining.
Best of luck! I hope it's resolved quickly. M.