The effects of sample presentation on near-infrared (NIR) reflectance spectra were examined. Using a Foss NIRSystems Rapid Content Analyzer, which uses sample cups for sample presentation, four important parameters were identified: cup diameter, sample thickness, cup material and packing method. Below a critical diameter of 20 mm, which is dependent on the detector geometry, the spectra became increasingly distorted (i.e., changes in spectral intensities and spectral shape, shifts in peak positions and occurrence of Wood's peak). The minimum sample thickness not to cause spectral distortion was dependent on the physical and chemical nature of the substance. A thickness > or = 10 mm was found to be adequate for most pharmaceutical excipients. The method of packing was also important. Tapping a powdered sample sometimes caused significant changes (P < 0.05) in the spectral absorbance values compared with simply pouring the sample into the sample cup. Standard sample cups made from quartz were to be preferred owing to their lack of background absorptivity. However, the two commercially available flat based vials examined, which were made from soda glass and clear neutral glass, proved to be as suitable for all except applications of the most exacting nature. The spectral distortions resulting from variations in cup diameter, sample thickness and cup material were also shown to alter significantly the values of two commonly used identification algorithms, correlation coefficient (< 0.95) and maximum distance (> 3.0 standard deviation distance), sufficiently to cause misidentifications.