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Glycerol-based epoxy networks have great potential for surface functionalization, providing anti-microbial and protein repellant function. However, the synthesis of glycerol glycidyl ether (GGE) monomer often requires excessive epichlorohydrin (ECH). ECH derived organochloride containing byproducts from monomer production maybe present in the eluent of the polymer networks prepared by cationic ring-opening polymerization. Here, the cytotoxicity analysis revealed cell damages in contact with the polyGGE eluent. The occurrence of organochlorides, which was predicted based on the data from high-performance liquid chromatography/electrospray ionization mass spectrometry, as confirmed by a constant chloride level in GGE and polyGGE, and by a specific peak of C–Cl in infrared spectra of GGE. The resulting polyGGE was densely crosslinked, which possibly contribute to the trapping of organochlorides. These results provide a valuable information for exploring the toxins leaching from polyGGE and propose a feasible strategy for minimizing the cytotoxicity via reducing their crosslink density. Graphic abstract The eluent of poly(glycerol glycidyl ether) (polyGGE) films impaired the viability and metabolic activity of L-929 cells due to the organochloride byproducts or epichlorohydrin precursors originating from the GGE monomer, which was predicted based on the data from high-performance liquid chromatography/electrospray ionization mass spectrometry (HPLC–ESI–MS) and confirmed by chloride content analysis and attenuated total reflection fourier transform infrared (ATR-FT-IR) spectroscopy.