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To study the fine structure of fragmentary marker chromosomes, we performed scanning electron microscopy (SEM) on samples isolated from two carriers (Case 1: 46, XY/47, XY, +mar/48, XY, +mar, +mar; Case 2: 47, XY, +mar). In both cases, light microscopic observation revealed that marker chromosomes lacked a centromere and were fragmented in appearance. However, SEM observation of the metaphasic cells in both cases showed three variations. One variation was a structure that seemed to be metacentric, another was a structure that seemed to be submetacentric, and the remaining one was essentially fragmentary. However, neither the usual chromatid nor centromere formations were observed in the metacentric-like and submetacentric-like structures, even when both cases were observed by SEM. Moreover, the marker chromosomes of the boy of Case I, who suffered from various clinical troubles, included a greater population of metacentric-like or submetacentric-like structures than of essentially fragmentary structures. The marker chromosomes of the fetus of Case 2, who suffered from no clinical problems, included a much greater population of essentially fragmentary structures than metacentric-like or submetacentric like structures. Therefore, SEM observation of fragmentary marker chromosomes that are visible on light microscopy might be used to define specific structures. Moreover, SEM observation might provide clinical criteria relating to the pathogenesis of fragmentary marker chromosomes found on light microscopy.