Abstract Petroleum geochemistry has historically relied on the analysis of field samples – source rocks, oils and gases. Data collected for individual samples are considered characteristic of a specific geographical location and geological position that, when aggregated with data from other samples, can be extrapolated to larger scales. These scale-ups may be as small as a few metres, such as a detailed characterization of source rocks penetrated by a single well, to global, such as petroleum systems that now span continents due to plate tectonics. However, a single sample contains a wealth of information at smaller scales. In situ analytical techniques have improved significantly over the last decade, allowing us to examine sedimentary rocks at ever higher spatial (areal and temporal) resolution. Mass spectrometric imaging is an emerging, enabling technology that can be performed at c. 200 µm (matrix-assisted laser desorption) to 50 nm (nanoSIMS) resolution. X-ray microcomputed tomography (µ-CT) is being applied to examine the storage and transport of petroleum in low-permeability shales and carbonates at spatial resolutions as low as c. 8 µm. Pore architecture in shale, both organic and inorganic, can be modelled from small-angle neutron scattering (SANS) data and imaged directly with helium ion microscopy at c. 1 nm resolution. Atomic force microscopy (AFM) can now resolve the molecular structure of individual asphaltene molecules. Information obtained with these techniques is now revealing the fundamental nature of geological organic materials, opening the span of petroleum geochemistry from atoms to continents.