Homoisoflavonoids, a special subclass of flavonoids, are rarely found in nature, mainly existing in Fabaceae and Asparagaceae families and being less common in Polygonaceae, Portulacaceae, Orchidaceae, and Gentianaceae families. Until now, approximately 240 natural occurring homoisoflavonoids have been identified from roots, barks, heartwood, bulbs, leaves, and seeds of the plants from the above mentioned families, which have often been used in traditional medicine. Homoisoflavonoids have been reported with a broad range of bioactivities, including anti-microbial, anti-mutagenic, anti-oxidant, immunomodulatory, anti-diabetic, cytotoxic, anti-angiogenic, vasorelaxant, and anti-inflammatory effects. To organize this review, the homoisoflavonoids were classified into five groups based on their structures: sappanin-type (I), scillascillin-type (II), brazilin-type (III), caesalpin-type (IV), and protosappanin-type (V). The structures of natural occurring homoisoflavonoids are described, and their proposed biosynthetic pathway and recent pharmacological studies are discussed. The main purpose of this review is to provide a comprehensive and up-to-date state of knowledge from phytochemical and pharmacological studies performed on homoisoflavonoids during the past decades. Homoisoflavonoids might have a large potential for further investigations of their bioactivities in order to identify important leads.