6-Methyl-5-cyanouracil is primarily used in the field of pharmaceutical research and development. It serves as a key intermediate in the synthesis of various biologically active compounds, particularly those with potential antiviral and anticancer properties. Its structure allows it to be incorporated into nucleoside analogs, which are crucial in designing drugs that target viral replication or cancer cell proliferation. Additionally, it is utilized in organic synthesis for creating derivatives that can be screened for therapeutic activity. Its applications extend to biochemical studies, where it aids in understanding enzyme mechanisms and interactions due to its ability to mimic natural nucleobases.