I am five days late but am not pregnant, what else coule be wrong? also my kidneys have been hurting really bad. are the two issues related?

Probably not related: There is no reason why a delayed period should be related to your kidney. Are you sure that your kidney is hurting? Could it be musculoskeletal? Suggest you see a physician. Kidney ultrasound is the easiest plus non-invasive way of checking out your kidneys.

Uncertain: Reasons for missed / late period include: an anovulatory cycle in which no egg is released, marked v or ^ in weight; eating disorder; Over-exercising (endurance athletics), stress, travel, significant illnesses, oral contraceptives & other meds, Illegal drug use, breast feeding, hormone imbalances and medical problems (i.e., PCOS). Pregnancy is #1 reason.