Three putative ciliate fossils were described from the Neoproterozoic Doushantuo Formation in China: Eotintinnopsis, Wujiangella, and Yonyangella. The identity of these fossils is important for our understanding of the origins and early morphological evolution within ciliate clades. Here we compare the homology of the fossil characteristics with those in their proposed ciliate relatives. Eotintinnopsis resembles a tintinnid, but its feathery tentacle-like apical structure is probably not homologous within any known ciliate. Wujiangella presents homology issues with the size and distribution of its putative somatic cilia. Yonyangella appears to be a suctorian with its tentaclelike structures, but the presence and size of its putative somatic cilia pose homology issues. We suggest that these three fossils are likely to be taphonomically and diagenetically distorted and altered acritarchs. These alterations include secondary mineral encrustations on the interiors of vesicles, the crushing, folding and other distortions of the vesicles, the bending and crushing of the acritarch spines, and the preservation of organic material in and outside of the cysts. The earliest known ciliate fossil remains a tintinnid that occurs in the Ordovician of Kazakhstan.