Two dimensional gel electrophoresis (2DE) and MALDI-TOF MS were used to obtain a global view of the cytoplasmic proteins expressed by Thermoplasma acidophilum. In addition, glycerol gradient ultracentrifugation coupled to 2DE-MALDI-TOF MS analysis was used to identify subunits of macromolecular complexes. With the 2DE proteomic approach, over 900 spots were resolved of which 271 proteins were identified. A significant number of these form macromolecular complexes, amongst them the ribosome, proteasome and thermosome, which are expressed at high levels. In the glycerol gradient heavy fractions, ten as yet uncharacterized proteins - besides the well-known ribosomal subunits, translation initiation factor eIF-6 related protein, elongation factor 1 and DNA-dependent RNA polymerase - were identified that are putative building blocks of protein complexes. These proteins belong to the categories of hypothetical or conserved hypothetical proteins, and they are present in the cytosol at low concentrations. Although these proteins exhibit homology to known sequences, their structures, subunit compositions and biological functions are not yet known.