Ciliary structure in Scaphopoda is hitherto unknown and may provide information useful for phylogenetic analyses. Here we describe the ultrastructure of the ciliary apparatus of multiciliated epidermal cells of four species of Scaphopoda: Antalis entalis, Antalis occidentalis, Entalina tetragona and Cadulus propinquus, revealed by transmission electron microscopy. In all studied species the cilia have long whip-like distal ends. The rootlet apparatus consists of a basal foot, a short anterior ciliary rootlet and a long vertical rootlet. In other molluscan classes, the presence of an anterior rootlet has previously only been shown in species of the Neomeniomorpha, Chaetodermomorpha and Polyplacophora, while such a rootlet is absent in Gastropoda, Bivalvia and Cephalopoda. Twin rootlets, such as present in species of lamellibranch Bivalvia and postembryonic Cephalopoda probably represent a split vertical rootlet. The discovery of an anterior rootlet in Scaphopoda shows that the presence of paired ciliary rootlets is not a synapomorphy of a clade comprising the aplacophoran Neomeniomorpha and Chaetodermomorpha and the Polyplacophora, but that it represents a plesiomorphy of the Mollusca.