Geochemical data from rock-cutting samples can give rise to faulty interpretations due to contamination from drilling fluids used in modern deepwater petroleum exploration. In this study, oil-based drilling contaminants were removed by solvent extraction with dichloromethane and methanol (9:1) solution. Bulk and molecular organic geochemical characteristics were examined for both oil-based drilling mud and cleaned rock-cutting samples. Total organic carbon (TOC) values are notably high in heavy liquid oil-based drilling mud mixtures (TOC = 21.4–63.3%, average = 34.6% ± 8.6) compared to cleaned rock cuttings (TOC = 0.4–1.5%, average = 0.8% ± 0.3). In addition, drilling mud mixtures contain higher concentrations of unresolved complex mixtures (UCM) in the n-alkanes fraction. Therefore, it is difficult to distinguish individual homologues in the n-alkanes fraction. The triterpanes also have relatively high UCM contents compared to steranes fractions. However, hydrocarbon homologues can be identified in both the triterpanes and steranes fractions of oil-based drilling mud mixtures. Gas chromatograms indicate that the n-alkanes fractions of rock cuttings initially cleaned with solvent still show considerable contamination from drilling fluids. This remaining contamination was removed by an additional cleaning step using the soxhlet extraction technique. The triterpanes fraction in solvent-cleaned rock cuttings does not contain an overprint of heavy liquid oil-based drilling mud contamination. However, solvent-cleaned rock cuttings may still retain contamination signatures at the sterane C28-20R homologue due to coelution. The geochemical overprint of contaminants in the cleaned rock cuttings can be interpreted as infiltration of lower molecular weight compounds into micro-cracks of the cuttings. The distribution of these molecules varies in each hydrocarbon fraction. Therefore, close inspection of contamination effects is required before interpretation of traditional organic geochemical proxies such as source rock characteristics and maturity.