The exploration of molecular recognition of synthetic macrocycles in aqueous media is significantly important since most biological functions, activities and processes take place in water. Pillar[n]arenes (n = 5-10) have been recognized as a new generation of macrocyclic arenes; much attention has been devoted to their host-guest chemistry. This review summarizes the host-guest properties of water-soluble pillararenes towards biologically significant molecules and drugs. These water-soluble pillararenes are classified into three major classes according to the electric charges of hydrophilic groups at their portals: anionic pillar [n]arenes (AP[n]s), cationic pillar[n]arenes (CP[n]s), and neutral pillar[n]arenes (NP[n]s). The host-guest affinities, binding modes, binding selectivity, stimuli-responsiveness, as well as biomedical applications are comprehensively discussed.