Trioxane based compounds such as artemisinin and its synthetic and semi-synthetic analogues constitute promising class of antimalarial agents. The pharmaceutical development of artemisinin was started in 1971 after the isolation from Chinese medicinal plant Artemisia annua and this compound has drawn much attention from medical chemist and pharmacologist worldwide. Researchers from across the globe have independently and collaboratively conducted various studies on the artemisinin system in an attempt to identify lead molecules for malaria chemotherapy. This systematic study led to the discovery of artemether, arteether, dihydroartemisinin, and sodium artesunate which are being used as antimalarial drug for the treatment of Plasmodium falciparum related infections. These studies also revealed that the trioxane bridge is essential for the antimalarial activity of this class of compounds. Another class of structurally simple peroxides that emerged from these studies was the 1,2,4,5-tetraoxanes. Some of the tetraoxane based compounds have shown promising antimalarial potential, and much of work has been done on this type of compound in recent years. Apart from their antimalarial activity, these classes of compounds have also shown promising anticancer and antibacterial activity. To this end, an attempt has been made to describe the medicinal potential of trioxane and tetraoxane-based compounds. Literature from 1999 has been critically reviewed and an attempt has been made to discuss structure activity relationship study among the series of trioxane and tetraoxane based compounds.