Kidney stones do not cause UTI, but if you have kidney stone you are at risk of developing UTI. Most bacteria that cause UTI are bacteria that are normally found in the bowel or normal flora in the bowel. Bacteria multiply until they can reach the upper urinary system. The urinary system’s natural way of flushing out bacteria is through passing out of urine, bacteria can be flushed out with urine. But the presence of kidney stones obstructs flushing out of urine and the bacteria. When bacteria are able to mix with urine, and urine cannot flow through the ureters because of a kidney stone, the pooling of infected urine in the kidney can cause pyelonephritis or infection in the kidneys.