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I also experienced problems with blood clots after surgery. The catheter was in for 7 days after surgery, and during that time, small clots came through the tube. After the catheter came out, clots continued, and 3 days later I experienced a blockage and couldn't pee. I was told to go to the emergency room, where they put in a new catheter which got everything flowing again. However, even with the new catheter, 2 days after that I was blocked up again, and back in the emergency room being irrigated. There were a lot of clots, some were as big as ants. That second catheter stayed in for two more days, and then the urologist removed it -- and everything has been fine since.
The urologist/surgeon said that I probably had a large scab develop inside my urethra after it was put back together, and the clots were the pieces of it working their way out. He said he sees this about once every 3 or 4 years (and he's done 100's and 100's of robotic prostatectomies).
The experience was very anxiety producing, especially seeing blood and clots in my urine and having to be awake for a new catheter to be put in. But, thankfully, it is all past me now!