Hydrocarbon contamination affects the performance of most vacuum dependent scientific apparatus. In the electron microscope contamination of the specimen due to polymerisation of backstreaming pump fluids and other system hydrocarbons, contributes to poor resolution. In surface analysis equipment (e.g. XPS, AES and UPS) hydrocarbon contamination may interfere with the analysis and in the mass spectrometer it can adversely affect resolving power and complicate interpretation of results. A combination of pumps is used to generate the vacuum required in scientific instruments. Pumping systems normally employ one or more of the following: rotary, diffusion, turbomolecular, ion, sublimation and cryo pumps. The main sources of contamination are directly attributable to these pumps, the construction materials used in the equipment and the processing of these materials. In an ultra-clean system the sample itself may introduce hydrocarbon contamination. Reduction of hydrocarbon contamination involves the use of traps (either cooled or absorbent), selection of special pump fluids, special processing techniques in the case of ion pumps and selection of system components, including resilient seals, which can be suitably processed to reduce contamination. Special techniques may be used to clean samples in situ. Experiments are described which show the sources of system contamination and remedies are suggested based on practical experience gained in design and operation of vacuum systems for electron microscopes, electron spectrometers, scanning transmission electron microscopes and mass spectrometers.