text: can a kidney infection effect a woman's menstral cycle? recently had a kidney infectionim now over it as far as i know but im now two days late on my period. im really worried about pregnancy although i always make sure my partner checks the condom to see if its broken. ofourse i understand that this worry could be causing stress and then may have effected my cycle also. am i late because of my kidney infection?? please help! yes of course it can.......there are countless things that can disturb the menstrual cycle.....with most urine infections there is a concentration of body fluids,....this causes your body to stop the production of some hormones.....it will pass after your infection is better....