Plants contain about 12 000 kinds of alkaloids. Alkaloids belong to small-molecule nitrogen heterocyclic compounds. The metabolic pathways of alkaloids are controlled by specific enzymes, and the locations of some key enzymes can determine the cellular and subcellular structure of specific cells where synthesis, transport and storage of alkaloid take place. Here we summarize findings for the isoquinoline alkaloid sanguinarine in biosynthesis, transport and storage functions at the cellular and subcellular levels. Biosynthesis of isoquinoline alkaloids mainly occurs in the cortex, sieve tubes, companion cells, and latex tubes. Vesicles, vacuoles, cytoplasmic matrix, microsomes, endoplasmic reticulum, and chloroplast thylakoid are involved in transport and storage. We discuss related results of several other types of alkaloids found in medicinal plants.