A variety of chemicals induce site-specific lesions in the rodent nasal cavity. In order to explore the reasons for this site-selectivity, methodology for (a) creation of a 3-dimensional (3D) model of a rat nasal cavity, and (b) mapping of semiquantitative data onto the model has been developed. The head of a rat was fixed, decalcified, step-sectioned (every 100 microm) and stained with hematoxylin and eosin. Digital images of the sections were optically captured, and a KS400 image analysis system (Imaging Associates, Thame, Oxford, UK), attached to a standard personal computer, was used to align adjacent images and reconstruct the series in 3D. The final model was anatomically correct, and could be rotated in any plane and manipulated to display individual internal structures. The spatial localization of a glutathione S-transferase (rGSTM1, previously known as GST 3-3) within this model was investigated using immunohistochemistry. Step sections (every 400 microm) were stained, analyzed by imaging densitometry, and the results for the stained regions within the nasal cavity divided into 4 grades representing high to low expression of rGSTM1. The data was mapped onto the 3D model and showed that the highest expression of this enzyme was in the central regions of the nasal cavity at the transition between respiratory and olfactory epithelia. This methodology will allow investigation of the relationship between the in situ localization of bioactivating and detoxifying enzyme systems and the site-specificity of nasal lesions.