Blood Clots in Urine. Blood clots in urine can be a sign of an internal injury that causes bleeding, inflammation, or disease. The medical term used for blood in the urine is hematuria. Blood clots in urine obviously result from large enough bleeding to turn the color of urine red and have visible clots. Visible presence of blood in urine is called gross hematuria. Some of the most common causes of blood clots in urine are kidney diseases or other urinary tract problems.