Observations on the hemichordate worm Protoglossus graveolens demonstrate that the gill slits, pre-oral ciliary organ (POCO), and the lining of the cylindrical pharynx are used in filter feeding. Pumping of water is generated by cilia that line the lateral gill bars and the POCO directs water from the dorsal surface of the proboscis to the mouth. Particles are trapped and concentrated on the primary and secondary gill bars and transported ventrally and posteriorly by cilia that line the pharynx. The oesophageal organ functions as a barrier to water flow and to squeeze excess water from the mucus-food cord. Particles that passed freely through the gill pores were a maximum of 1.28 µm in size. Diluted milk entered the mouth and was pumped through the pharynx at a rate up to 4.05 mm s−1. The Reynolds number and propulsive efficiency of the filter-feeding structures are estimated using algebraic models. Protoglossus elegantly orchestrates the movements of food particles captured by simultaneous filter feeding and deposit feeding or may, from one moment to the next, switch back and forth between deposit and filter feeding. Structural and functional similarities with the cephalochordate pharynx suggest that a wheel organ/ POCO and a filter-feeding pharynx may have been present in the common ancestor to the deuterostomes. © 2009 The Linnean Society of London, Biological Journal of the Linnean Society, 2009, 98, 898–906.