Analysis of the molecular composition of the organic matter (OM) from whole sediment samples can avoid analytical bias that might result from isolation of components from the sediment matrix, but has its own analytical challenges. We evaluated the use of GCxGC-ToFMS to analyze the pyrolysis products of six whole sediment samples obtained from above, within and below a 1 million year old OM-rich Mediterranean sapropel layer. We found differences in pyrolysis products <n-C (sub 22) between the OM-rich sapropel samples and the OM-poor background marls. The presence of alkyl pyrroles, probably derived from chlorophyll, in pyrolysates of the sapropels but not in those of the marls suggests that higher marine productivity and greater OM preservation accompanied deposition of the sapropels. Detection of tetramethyl benzenes considered to be pyrolysis products of isorenieratene in the sapropel samples is evidence that nitrogen-fixing green sulfur bacteria contributed to the high productivity. Greater abundances of shorter chain aliphatic hydrocarbons, pyrroles, furans and alkyl aromatics in the pyrolysates of sapropel samples relative to the marls confirm better preservation of marine OM in the sapropels. In addition, the presence of greater amounts of thiophenes in the sapropels than in the marls is consistent with the existence of euxinic conditions during sapropel deposition. The combination of whole sediment pyrolysis and GCxGC-ToFMS is promising, but the procedure requires careful selection of its multiple analytical variables, particularly the pyrolysis temperature and the operational features of the GC columns. Abstract Copyright (2011) Elsevier, B.V.