Drug delivery systems that can deliver therapeutic and/or diagnostic agents to the colon are disclosed. The systems include pectin beads crosslinked with zinc or any divalent cation of interest, which beads are then coated with Eudragit®-type polymers. The drug delivery systems are orally administrable, but can deliver the active agents to the colon. In some embodiments, they can administer the agents to various positions in the gastro-intestinal tract, including the colon. The agent can be a small molecule, peptide, protein, nucleic acid, or complex structures of natural, recombinant or synthetic origin. In still other embodiments, the agent is a diagnostic agent. The agents can be used to diagnose, treat or investigate humans and animals for a variety of conditions, including infectious diseases, inflammatory diseases, cancers and the like. Colon-specific delivery is obtained by formulating a prophylactic, therapeutic, and/or diagnostic agent with specific polymers that degrade in the colon, such as pectin. The pectin is gelled/crosslinked with a cation such as a zinc cation. The formulation, typically in the form of ionically crosslinked pectin beads, is subsequently coated with a specific polymer such as a Eudragit® polymer. Processes for obtaining such beads are also disclosed.