The brain relies on the blood-brain barrier (BBB) for the selective absorption of nutrients and the exclusion of other big molecules from the circulating blood. Therefore, the integrity of BBB is critical to brain health, and assessing BBB condition is of great clinical importance. BBB is often examined using exogenous tracers that can travel across the BBB, but the tracers might cause severe side effects. To avoid the use of external tracers, researchers have used magnetically labeled arterial blood as the endogenous tracer to assess the water permeability of BBB as a surrogate index of BBB. This paper reviews the three major types of arterial spin labelling-based BBB water permeability assessment techniques and their applications in brain diseases such as Alzheimer’s disease.