The influence of the chain sequence structure of an alternating ethylene-tetrafluoroethylene (ETFE) copolymer and poly(vinylidene fluoride) (PVDF) on both positive and negative time-of-flight secondary ion mass spectrometry (ToF-SIMS) spectra (m/z less than or equal to 200) was studied. The C-1, C-2, C-3, C-4 and C-5 positive ions were found in the ETFE spectrum, while only the C-1, C-2 and C-3 positive ions were found in the PVDF spectrum. These results indicate that ETFE can be distinguished from PVDF by the presence of its characteristic C-4 and C-5 positive ions. Even though both ETFE and PVDF produce some of the same C-3 positive ions, these positive ions come from different sequence structures. The negative ToF SIMS spectra of both ETFE and PVDF are totally dominated by F- (m/z = 19) because F- is very stable, due to its largest electronegative value, and fluorine concentration in ETFE and PVDF is relatively high. These results indicate that the chain sequence structure has a significant effect on the positive ToF-SIMS spectra of ETFE and PVDF, especially in the high-mass range. However, the chain sequence structure does not have much effect on the negative spectra of ETFE and PVDF.