We determined the structure of the Schizosaccharomyces pombe centromere cen3 using direct genomic mapping and cosmid walking. The repetitive region of cen3 is approximately 110 kb, much longer than that of the previously determined cen1 and cen2 regions. The approximately 30 kb long left and approximately 60 kb right repetitive sequences are arranged with an inverted symmetry and flank the 15 approximately 20 kb central domain. The repeat motifs in cen3, although they consist of the common centromeric repeat elements, are slightly different from those in cen1 and cen2. The cen3 repeat motifs appear to be reiterated four times in the left and nine times in the right side repetitive regions. We found that the central domain consists of the common approximately 5 kb core sequence associated with the pair of innermost inverted sequences, most of which are reiterated only twice in the genome. Although their sizes differ significantly, the general features of cen1, cen2 and cen3 are similar, and a prototype, consensus structure for the fission yeast centromere may be deduced.