Near-surface sediments (0–45 mm depth interval) from the Iceland Basin (59°N, 21°W, 3070-m water depth) and Biscay Abyssal Plain (48°N, 17°W, 4105-m water depth) were sectioned at millimeter-scale resolution to assess alterations in key lipid biomarkers during early diagenesis. Inventories (µg cm−2 in the topmost 45 mm) of biomarkers from presumed terrestrial sources (>C20 linear n-alkanes, n-alkanoic acids, n-alkanols) and from phytoplankton sources (phytosterols, long-chain alkenones and alkenoates) were 1.5–4 times more abundant in the Iceland Basin core than in the Biscay Abyssal Plain core, indicating greater sedimentary inputs and/or preservation at the Iceland Basin site. Biomarker concentrations varied significantly over millimeter-scale depth intervals. Pronounced subsurface concentration maxima were present at both sites. At the Biscay Abyssal Plain site, steep concentration gradients in the uppermost few mm of the sediment column indicate extensive diagenetic losses at or near the sediment/water interface. Strong covariance was seen in the concentrations of various compounds within each class (e.g., long-chain n-alkanes, n-alkanols, n-alkanoic acids and long-chain alkenones and alkyl alkenoates), indicating that individual compounds within each class are associated with the same organic matrix and have similar degradation and mixing rates. Thus biomarker indices for assessment of land-derived inputs (CPI, C29/C31, ACL) and sea surface temperature (IPT) remain largely unaltered by early diagenetic processes in oxic, abyssal sediments in spite of extensive bioturbation and degradative losses within the uppermost few centimeters of the sediment column.