The surface net hydrophobicity and local hydrophobicity of green fluorescent protein was evaluated by using the aqueous two-phase partitioning method. The surface net hydrophobicity of GFP allowed it to be classified as a hydrophobic protein although the local hydrophobicity was low. The local hydrophobicity of the GFP was increased by a pH shift to acidic conditions and was maximal at pH 4. The surface net hydrophobicity increased at acidic conditions less than pH 4. The conformational change of GFP at acidic pH is discussed based on the above results.