Fourier-transform infrared (FT-IR) spectroscopy was employed to investigate potential lyophilization-induced changes in the secondary structure of lipases from Candida antarctica B and Pseudomonas cepacia. The secondary structure elements were determined by curve fitting of the amide III bands of the two lipases in the lyophilized state in KBr pellets and in solution. It was found that lyophilization decreased the alpha-helix and increased the beta-sheet content. However, FT-IR analysis of crosslinked enzyme crystals of Pseudomonas cepacia lipase also indicated an increase in the beta-sheet content, which appears despite the fact that the enzyme, being in the crystallized state, should possess native conformation. This result partially questions the suitability of FT-IR for analysis of the structure of solid proteins, at least as far as the beta-sheet content is concerned, because it is possible that the method overestimates the beta-sheets by measuring other hydrogen-bonded nonperiodic intermolecular structures. No significant modification was observed when lipase from Pseudomonas cepacia was lyophilized in the presence of methoxypoly(ethylene glycol).