Deoxypodophyllotoxin is primarily used as a key intermediate in the synthesis of anticancer drugs, particularly in the production of etoposide and teniposide. These derivatives are widely employed in chemotherapy to treat various types of cancers, including lung cancer, testicular cancer, and leukemias.

The compound itself exhibits strong antitumor and antiviral activities by inhibiting microtubule assembly, which disrupts cell division in rapidly proliferating cells. Due to this mechanism, it also serves as a lead compound in the development of novel cytotoxic agents.

Additionally, deoxypodophyllotoxin has shown potential in dermatological applications, such as in the treatment of genital warts caused by human papillomavirus (HPV), owing to its ability to induce apoptosis in infected cells. Its natural origin and potent bioactivity make it valuable in both pharmaceutical research and clinical therapeutics.