MALDI/TOF mass spectra of fluoropolymers have been reported to be very difficult to obtain, with the few successful reports being on functionalized materials and relying on the use of special fluorinated matrices. Herein, we will report upon the successful MALDI/TOF mass spectral characterization of a group of important, inert fluoropolymers, namely non-functionalized perfluoropolyalkylethers (PFPAEs) as well as some of their functionalized derivatives. The results show that with the proper selection of cationization agent and solvents and with the proper procedures of target preparation, inert PFPAEs can be characterized with common matrices such as a-cyano-4-hydroxycinnamic acid (CCA) and 2,5-dihydroxybenzoic acid (DHB). The performance of these routinely used matrices proves to be as good as, if not better than fluorinated matrices. In addition, the MALDI mass spectra can provide important information on these commercial PFPAEs including their repeat units, end groups, molecular weights, and molecular weight distributions. MALDI/TOF mass spectrometry can readily distinguish between dilute samples of structurally similar PFPAEs within a short period of time. Thus, MALDI/TOF mass spectrometry should be adaptable for routine quality control during both the manufacture and use of PFPAEs.