Few data exist regarding the protein composition of idiopathic epiretinal membrane (iERM). In the present study we compared the proteome of epiretinal membrane of iERM with the proteome of the inner limiting membrane (ILM) of idiopathic macular hole (iMH). Twelve epiretinal membrane samples were obtained from patients with iERM undergoing therapeutic vitrectomy. Twelve ILM samples from patients with iMH were used as controls. Proteomic analysis was conducted with discovery-based label-free quantitative nano-liquid chromatography - tandem mass spectrometry (LFQ nLC-MS/MS). Verification of results was performed with targeted MS using selected reaction monitoring on a different set of samples. Discovery data were searched against the Uniprot Homo sapiens protein database using MaxQuant Software. Identified proteins were filtered with Perseus software. Bioinformatic analysis of the differences in protein expression between epiretinal membrane from iERM and ILM from iMH was performed using STRING. A total of 2,183 different proteins were identified. 357 proteins were found to be present in all samples. The protein profile of iERM was highly different from iMH with 62 proteins found at significantly higher levels in iERM. The proteins upregulated more than 10-fold in iERM were: fibrillin-1, tenascin, prolargin, biglycan, opticin, collagen alpha-1(II) chain, protein-glutamine gamma-glutamyltransferase 2, fibronectin, filamin-A, collagen alpha-2(IX) chain, spectrin alpha chain, transforming growth factor beta induced protein ig-h3, dihydropyrimidinase - related protein 3, endoplasmin and glutamate dehydrogenase 1. Proteins with high level in iERM consisted of proteins that especially localized to the actin cytoskeleton, the extracellular matrix and the mitochondrion. Analysis of all proteins indicated that the disease process in iERM at least in part can be characterized as skin formation with perturbation of nucleotide metabolism. Our study identified proteins that have not earlier been associated with iERM. Fifteen proteins are found at very high concentration, 10-fold or more, and amongst these four proteins, fibrillin-1, tenascin, prolargin and biglycan were found at more than a 100-fold higher content compared to ILM of iMH. These proteins may be potential therapeutic targets. Data are available via ProteomeXchange with identifier PXD014286.