Analysis of F2-isoprostanes in urine using gas chromatography-mass spectrometry is confounded by the presence of endogenous compounds interfering with the internal standard, 15-F2t-IsoP-d4 (m/z 573). Previous efforts to resolve the 15-F2t-IsoP-d4 from co-eluting peaks with different solid phase extractions were unsuccessful. This study has now used a highly-deuterated, d9-analogue of the derivatization agent N,O-Bis(trimethyl-d9-silyl) trifl uoroacetamide (BSTFA-d9) yielding trimethylsilyl ethers, but this was not successful in resolving the 15-F2t-IsoP-d4 from co-eluting peaks. It was hypothesized that interfering peaks at m/z 573 could be the tetrahydro analogue of 15-F2t-IsoP. However, using an authentic standard showed the interfering peaks are not due to this metabolite. In subsequent experiments good resolution was shown of the 15-F2t-IsoP peak using 8-F2t-IsoP-d4 (m/z 573) as the internal standard. These data show that care must be taken when using GC-MS for quantitation of F2-IsoPs to prevent interfering substances affecting the results.