The process by which diseases, particularly neoplastic diseases, are diagnosed by pathologists using microscopic evaluation of tissue has changed little over the last several decades despite the advent of molecular medicine. Cells or tissues, stained with complex and sometimes poorly characterized organic dyes, are examined using a subjective, pattern-matching approach whose accuracy and reproducibility has increasingly been challenged. Furthermore, the ability of pathologists to deliver accurate prognoses using histological and clinical parameters remains limited, leading to both over- and under-treatment. While molecular techniques hold out great promise as diagnostic and prognostic tools, they are currently still largely investigational, and costly. A complementary approach is proposed, whereby more information is obtained by improved analysis of conventionally prepared histological and cytological samples. Using inverse Fourier transform multi- pixel spectroscopy, a new instrument has been developed which can display a complete transmittance or emission spectrum at every pixel of an image, providing much more color information than can be appreciated by eye or by conventional red-green-blue color cameras. Since spectra variations in staining behavior correlate with alterations in subcellular macromolecular composition it seems likely that they may also correlate with diagnosis and clinical behavior for a number of disease states. Examples of how this approach may prove useful in clinical practice are provided.