Apart from kidney stones, blood in the urine is also an indication that your kidneys are not in good shape. Several kidney diseases can cause blood in the urine, including glomerulonephritis, pyelonephritis, and kidney cancer. Glomerulonephritis is an inflammation of the filters in the kidneys, while pyelonephritis is an infection of the kidneys. Both conditions can damage the kidneys and lead to bleeding. Kidney cancer can also cause blood in the urine, although this is less common.