Extending our previous efforts to characterize ovarian neoplasms by interphase cytogenetics, we analyzed a series of 32 mucinous tumors by nonisotopic in situ hybridization with seven different centromere-specific probes as well as by flow and image DNA cytometry; we then compared the data with results of p53 and Ki67 immunohistochemistry and MYC DNA-PCR analysis and of the clinical follow-ups. Of the tumors studied, 11 of 14 (78.6%) mucinous carcinomas, 7 of 7 (100%) mucinous tumors of low malignant potential (LMP), and 7 of 11 (63.6%) mucinous cystadenomas demonstrated chromosomal aberrations. The mean number of chromosomal aberrations (+/- SD) was slightly higher in DNA cytometrically nondiploid cases than in diploid cases (2.0 +/- 1.6 versus 1.6 +/- 1.2, not significant) but did not differ significantly among the study groups (carcinomas: 1.7 +/- 1.4; tumors of LMP; 1.9 +/- 0.7; adenomas: 1.4 +/- 1.4). Aberrations affected chromosomes 1 (14 of 27 cases) and 6 (12 of 31) most frequently, followed by chromosomes 17 (7 of 28), 7 (6 of 29), and X (6 of 28). Signal gain for centromere 1, which was the most prevalent finding (13 of 27), was observed in 3 of 10 mucinous cystadenomas, 2 of 4 mucinous tumors of LMP, and 8 of 13 mucinous carcinomas. All six moderately and poorly differentiated carcinomas demonstrated this aberration. Signal gain of centromere 6 (3 of 13) and centromere 7 (4 of 13) were found only in carcinomas (p < 0.05 and p < 0.025, respectively). The interphase cytogenetic results correlated neither with proliferative activity, immunohistochemical p53 accumulation, MYC DNA amplification, nor postoperative outcome. Compared with serous ovarian neoplasms (Lab Invest 1996, 75:473-485), mucinous tumors demonstrated signal gain for chromosome 1 (p < 0.0001) and signal loss for chromosomes 6 (p < 0.001) and X (p < 0.01) significantly more often. Loss of centromere 17 was more characteristic for serous than for mucinous carcinomas (p < 0.05). Our observations show that chromosomal aberrations in mucinous ovarian neoplasms are apparently not random. These results support the notion that the molecular genetic changes in mucinous neoplasms differ from those in serous tumors.