The computer-assisted measurement of the standard deviation of the nucleolar area from pathologic slides of uveal melanomas correlates strongly with prognosis, but the eye must be removed and examined histologically. Because it is possible to perform fine-needle aspiration biopsies of intraocular tumors, we designed a study to determine if a fine-needle aspiration biopsy sample yields the same prognostic information as the enucleation specimen. In comparing the standard deviation of the nucleolar area measured from a fine-needle aspiration biopsy sample obtained from 53 freshly enucleated eyes with the standard deviation of the nucleolar area measured from the matched enucleation specimen, we found only a modest correlation (r = 0.57) between the two measurements. A t-test of matched pairs indicated a significant difference between the two measurements (P less than .01). The fine-needle aspiration biopsy technique does not yield the same prognostic information as the larger enucleation specimen because fine-needle aspiration biopsy material may not be representative of the tumor.