A large number of proteins involved in calcium and intracellular pH signaling and homeostasis have previously been discovered and characterized in Saccharomyces cerevisiae, Homo sapiens and Arabidopsis thaliana,but relatively few have been identified in Aspergillus species. The aim of this study was to identify proteins regulating the intracellular concentration of calcium ions and protons in Aspergillus spp. and compare these with other fungi. For Aspergillus spp. we identified 46, 97 and 105 putative Ca2+-permeable channels, cation/proton transporters and P-ATPases, respectively, the majority of them previously unknown. The subunits composing V-type H+ ATPase and F0F1 ATP synthase (F-type ATPase) from Aspergillus spp. were identified. The greater redundancy of Ca2+-permeable channels, cation/proton exchangers and P-ATPases in filamentous fungi (between 28 putative proteins from A. clavatus and 34 from A. oryzae)compared to that of S. cerevisiae (19 proteins) reflects a more complex cellular organization and filamentous growth form. On the other hand the complexity of V-type H+ ATPase and F0F1 ATP synthase in filamentous fungi is comparable to that in ascomycetous yeast species indicating that both ATPase complexes are a basic universal requirement of the fungal cell.