Anoplocephala perfoliata is a common tapeworm in horse with an ability to cause colic and increase mortality. At present, current diagnostic methods are not sensitive enough to detect A. perfoliata and immunoreactive excretory/secretory (E/S) proteins produced by this parasite, which comprise the most promising candidates for diagnostic tests. Here, we compared the E/S proteins produced by A. perfoliata worms of two different physiological states (small- and large-sized worms) in vitro by label-free quantitative (LFQ) proteomics with protein database composed of proteins encoded by Hymenolepis diminuta, Echinococcus multilocularis/granulosus and Taenia aseatica for protein identifications. The quantitative proteomics data was complemented with one-dimensional gel electrophoresis combined with immunoblotting using antisera from horses diagnosed positive and negative for this tapeworm. Protein bands cross-reacting most efficiently with the anti-A. perfoliata antibodies were subjected to in-gel digestion with LC-MS/MS identification. Both the non-gel and gel-based proteomic results were compared to propose a list of candidate proteins for further studies. These proteins will be validated for their suitability as diagnostic markers specific to cestodes and A. perfoliata.