Used as an intermediate in the synthesis of pharmaceuticals and agrochemicals, 1,3,6-Trichloroisoquinoline serves as a building block for more complex heterocyclic compounds. Its reactive chlorine atoms allow for selective substitution reactions, making it valuable in the development of bioactive molecules. It is particularly useful in medicinal chemistry for constructing isoquinoline-based scaffolds that exhibit antimicrobial, antiviral, or anticancer activities. Additionally, it finds use in the preparation of dyes and functional materials due to its stable aromatic structure and derivatization potential.