We have evaluated the effects of acetonitrile on the structure and function of bovine carbonic anhydrase II. The potential structural and functional changes in carbonic anhydrase in the presence of different acetonitrile/buffer ratios (0%, 17.5% and 47.5% v/v) were determined using a variety of methods. These included simple spectrophotometric methods to record enzyme velocity, fluorescence measurements and calculation of accessible surface area (ASA) to identify possible alterations in tertiary structure of the protein, CD measurements to search for secondary structure conversions, and thermal scanning to determine structural stability of the protein in different media. The Far-UV CD studies indicated that carbonic anhydrase, for the most part, retains its secondary structure in the presence of acetonitrile. Fluorescence measurements using iodide ion and ANS along with ASA calculations revealed that in the presence of acetonitrile some degree of conformational change occurs in the carbonic anhydrase structure. In addition to the hydrophobic pockets, two additional tryptophanyl residues become exposed to the solvent, thereby increasing the surface hydrophobicity of the protein. These alterations dramatically reduce the catalytic activity, thermal stability, and aggregation velocity of the enzyme. Thus, our results support a molten globule-like structure of carbonic anhydrase in the presence of acetonitrile.