The technique of Hadamard transform microscopic fluorescence imaging is described. With an Acridine Orange (AO) staining cell, some factors that influence the fluorescence intensity of a cellular AO-DNA complex were studied; thereby the technique was applied to measure the nuclear DNA content (ploidy) in a breast tumor cell, and some parameters were employed to evaluate the tumor malignancy. A comparative study with conventional microfluorometry indicates that our system has some outstanding advantages. By using this system, the results of malignancy evaluation for 38 cases of breast tumor specimens were concordant with pathological diagnosis. This work demonstrates that this technique has a high potential value in medicine and cytobiology and may be applied as a new method for diagnostic and prognostic studies of tumor cases.