Infrared spectroscopy which has traditionally been utilized by chemists and physicists for characterization and identification of the structural properties of chemical compounds is now becoming more relevant as a biodiagnostic tool. Recent reports suggest that arthritis and Alzheimer's disease can be diagnosed by using this technique. Changes associated with these diseases diagnosable with this technique are generally overt. In this study we have used 'Fourier transform infrared spectroscopy' (FT-IR) to analyze subtle changes in composition and structure of lipids and proteins in lung tissue, bronchoalveolar lavage and purified lamellar body fraction of mice exposed to methylmercury. Infrared measurements were made in attenuated total reflection mode using the Split Pea (Harrick Scientific Corporation, USA). Mice were treated with 4 doses of methylmercuric chloride (15 mg/kg body weight/dose), and control animals received an equivalent volume of physiological saline. Comparison of the control and experimental spectra revealed alterations in the intensities and frequencies of vibrational modes of lipids following methylmercury exposure. Results indicate that FT-IR spectral analyses may be a valuable tool for detecting subtle variations in biological components associated with drug exposure to lungs and, in particular may be very useful for assessing changes in bronchoalveolar lavage.