Systematic protein expression studies in the brain of exercising and sedentary animals have not been carried out for far. Signaling proteins are main structures regulating hippocampal function and we decided to determine differences in signaling protein levels in rat hippocampus by a proteomic approach. Aged, male Sprague-Dawley rats, 23 months old, were used for the study: the first group consisted of sedentary rats, the second of rats with voluntary exercise from 5 to 23 months and the third was performing involuntary exercise on a treadmill from 5 to 23 months. 2-DE with subsequent mass spectrometrical identification of spots followed by quantification of spots was carried out. Annexin A5, A3, phosphatidylethanolamine-binding protein, guanine nudeotide-binding protein G(I)/G(S) /G(T), 14-3-3 protein gamma, 14-3-3 protein zeta/delta, prohibitin, visinin-like 1, protein phosphatase 1, septin 8, phosphoprotein enriched in astrocytes 15, transcription factor Pur-beta, EEA1 protein, SH3 domain-binding glutamic acid-rich-like protein 2, and cell division cycle 42 showed differential protein levels in the three groups. These results form the basis for functional studies elucidating mechanisms and links between exercise and hippocampal signaling and function.