The elemental composition of marine sediment provides useful information for the study of environmental processes including biogeochemical cycling and contaminant partitioning. It is common practice to acidify marine sediment samples to remove carbonate before measuring the concentrations of organic carbon (C). To date, however the effects of acidification on the concentrations of hydrogen (H), nitrogen (N), sulfur (S) and oxygen (O) in marine sediments have not been explicitly addressed. Acidification may contaminate or alter the sediment samples and create experimental artifacts affecting the validity of resulting H/C, C/N and O/C ratios. The objective of this study was to quantify how various preparation techniques affect the measured concentrations of C, H, N, S and O in marine sediments. Effects of four different pretreatments: unacidified (whole), acidification by HCl vapor, acidification by direct addition of HCl, and combustion were evaluated using five marine sediments and a standard reference material. The magnitude of carbonate loss between the vapor and direct acidification treatments was evaluated using stable C isotope analysis. Carbonates were most effectively removed by direct addition of HCl; and our results agree with findings of other studies which found direct addition of HCl to be the most accurate method for measuring organic C. However, the acid treatments elevated the apparent concentration of H and O; and in a few cases concentrations of N and S were significantly affected by acidification. In general, combustion significantly reduced all elemental concentrations compared to the whole sample. Based on these results, we recommend analysis of the untreated whole sediment for determining N, H, O, and S.