Modern members of the mammalian order Cetacea (whales, dolphins and porpoises) are obligate aquatic swimmers that are highly distinctive in morphology, lacking hair and hind limbs, and having flippers, flukes, and a streamlined body. Eocene fossils document much of cetaceans' land-to-water transition, but, until now, the most primitive representative for which a skeleton was known was clearly amphibious and lived in coastal environments. Here we report on the skeletons of two early Eocene pakicetid cetaceans, the fox-sized Ichthyolestes pinfoldi, and the wolf-sized Pakicetus attocki. Their skeletons also elucidate the relationships of cetaceans to other mammals. Morphological cladistic analyses have shown cetaceans to be most closely related to one or more mesonychians, a group of extinct, archaic ungulates, but molecular analyses have indicated that they are the sister group to hippopotamids. Our cladistic analysis indicates that cetaceans are more closely related to artiodactyls than to any mesonychian. Cetaceans are not the sister group to (any) mesonychians, nor to hippopotamids. Our analysis stops short of identifying any particular artiodactyl family as the cetacean sister group and supports monophyly of artiodactyls.