The balance between the human body and surrounding microorganisms is crucial for homeostasis and health. A disturbance in host-pathogen interactions causes disease. Two important diseases of the kidney and urinary tract are directly caused by bacteria or bacterial toxins: urinary tract infection (UTI) and diarrhea-associated hemolytic uremic syndrome (HUS). In the majority of cases, UTIs are caused by bacteria ascending from the perineum through the urethra to the urinary tract. In contrast, HUS is caused by non-invasive bacteria, such as enterohemorrhagic Escherichia coli, which colonize the gut and do not enter the blood stream. In this latter case, the bacteria release Shiga toxin, which binds to blood cells and thus reaches the target organs, mainly kidneys. Interactions between Shiga toxin, blood cells and endothelial cells in the kidney lead to cell apoptosis and inflammation. Innate immunity and the antimicrobial peptide cathelicidin seem to play important roles in the pathogenesis of both UTI and HUS. Moreover, influencing cathelicidin production and release might offer new therapeutic and prophylactic strategies for both diseases.