As an early and sensitive source of biomarker library, urine is attracting increasing attention from researchers in different fields. The urinary proteome is being explored for their diagnostic capabilities, ability to monitor disease and prognostic utility. However, the urine component is extremely complicated mainly due to the disturbance introduced by various conditions, including intrinsic and extrinsic factors. Intrinsic factors including gender, age and daily rhythms are usually appreciated in clinical biomarker studies, but external factors are rarely taken into consideration. In this review, the effects of common extrinsic factors such as drugs, diet, physical activity, and extreme environments on human urine are summarized and discussed. These factors and the corresponding influence should be emphasized when biomarker studies are conducted. It will facilitate us to avoid costly phony candidates.