Objective：To establish a two-dimensional eletrophoresis system for total brain stem proteins of seasickness adaptive and non-adaptive rats and to identify the differentially expressed proteins for investigation of the possible mechanism of seasickness adaptation. Methods： According to the kaolin intakes after seasickness stimulation, 30 rats were divided into nonseasickness group （n= 10）,seasickness adaptive group （n=12） and seasickness non-adaptive group （n=8）. Another 10 normal rats not receiving stimulation were taken as blank control. The brain stem proteins of seasickness adaptive and seasickness nonadaptive rats （n= 6） were isolated by two-dimensional electrophoresis; the differentially expressed proteins were identified by peptide mass fingerprint （PMF）. Results： During a 21-day stimulation, the amount of kaolin consumption in seasickness adaptive rats experienced an increasing phase and a subsequent decreasing phase; seasickness non-adaptive rats consumed significantly more kaolin during the whole 21-day stimulation than the blank control rats did （P〈0.01 or P〈0.05）. Nine seasickness adaptive proteins were identified by PMF： peroxiredoxin Ⅰ , peroxiredoxin Ⅱ,light molecular-weight neurofilament, ubiquitin carboxyl-terminal hydrolase PGPg. 5, and glutamine synthetase were highly expressed ; carbonic anhydrase Ⅱ , triosephosphate isomerase Ⅰ , phosphoglycerate mutase isozyme B and mitochondrial voltage dependent anion channel were lowly expressed. Conclusion： Adaptation to seasickness can induce changes in the protein expression pattern of brain stem in the seasickness adaptive rats, which may be associated with energy metabolism, neurotransmitter adjustment and oxidative stress.