Flow cytometric analysis of DNA content using paraffin-embedded materials has become an important diagnostic, as well as prognostic, method for clinical pathology and investigative oncology. DNA content as measured in paraffin-embedded materials is closely related with that obtained from fresh specimens. This method also permits retrospective analysis on a lot of cases and studying different specimens of a tumor for intratumor heterogeneity. Flow cytometry was used to investigation of the DNA distribution in biopsy specimens from 30 patients with squamous cell carcinoma of the larynx. These patients had initially treated in our institute in the period from 1986 to 1988 and followed for two to four years. A modification of Hedley's method was used to prepare paraffin-embedded materials. DNA histogram were assessed in terms of DNA index (DI). The coefficient of variation for determination of DI ranged 4.2 to 13.7% (mean 7.8 +/- 2.4%). Using infiltrated lymphocytes and mesenchymal cells as an internal standards, aneuploid DNA histogram were found in 13 of 30 specimens (43.3%). DI ranged from 1.05 to 1.22. There was no significant correlation between DNA content and sex, age, tumor size, staging or treatment. The aneuploidy was found in 2 of 17 cases with well differentiated tumor (11.8%), 10 of 12 with moderately differentiated tumor (83.3%), one with poorly differentiated tumor (100%). 11.8% of patients with diploid tumor cells had recurrence during the interval of observation, compared to 38.5% of those with aneuploid tumor cells (p less than 0.05). In T1 lesions of glottic cancer aneuploid group had a significantly lower local control rate than diploid group (p less than 0.01).(ABSTRACT TRUNCATED AT 250 WORDS)