To data, there have been no comprehensive cytogenetic studies of mucinous colorectal carcinomas (MUCs). We used comparative genomic hybridization (CGH) and laser scanning cytometry (LSC), to analyze cytogenetic changes in 21 MUCs and to compare the results with those of our previous study of 60 non-MUCs. Six of 21 MUCs were aneuploid and 15 were diploid. Gains of 13q, 8q, 2q, 12p and 18p were more frequent aberrations. Recurrent decreases in DNA copy number were found frequently at 17p, 22q, 1p, 16p and 8p. Amplifications of 8q, 5p, 12, 18p, 13q and 20p were observed in aneuploid tumors. The average number of DNA sequence copy number aberrations (DSCNAs) was significantly higher in aneuploid MUCs than in diploid ones. Aneuploid MUCs were clinicopathologically more aggressive, with greater lymph node involvement, distant organ metastasis, recurrence after surgery, higher stage and poorer prognoses. Gain or amplification of 18p was detected in 5 of 6 aneuploid MUCs but not in diploid MUCs or non-MUCs. When the average number of DSCNAs was compared among MUCs and well, moderately, and poorly differentiated adenocarcinomas, the average number of DSCNAs was significantly lower in diploid MUCs; however, with aneuploid tumors, the average number of DSCNAs in MUCs was similar to that in poorly differentiated adenocarcinomas but higher than that in well and moderately differentiated cancers. Moreover, tumor cells were well differentiated in diploid MUCs but poorly differentiated in aneuploid MUCs. These data suggest that MUCs have two types with different genetic pathways, histologic characteristics, and behavior.