In this study clinical studies were conducted on galactosyltransferase associated with tumour (GAT) as a newly developed marker of ovarian cancers. The positive rates of GAT with a cut-off value of 16 U/ml (which corresponds to the mean + 2 standard deviations (S.D.) for healthy females) were 4.7% for benign ovarian tumours, 4.5% for endometriosis and 45.9% for ovarian cancers. GAT showed a positive rate comparable to that of CA546 or CA72-4 among other tumour markers (CA602, CA125, CA546, CA72-4, STN and SLX) examined in ovarian cancers. However, it showed lower positive rates for benign ovarian diseases and, in particular, it gave the lowest positive rate for endometriosis among the aforementioned tumour markers. Furthermore, the receiver operating characteristic (ROC) analysis for discriminating between ovarian cancer and endometriosis showed a significantly high area under the curve (AUC) for GAT compared with that of the other markers. GAT showed the lowest correlation coefficients with other markers, and the positive rate and the diagnostic efficiency were increased by its combination assay with CA602 and/or CA546. Furthermore, the accuracy of the diagnosis of ovarian cancer improved by examining GAT after screening with CA602 or ultrasonography. These results suggest that GAT is a suitable marker for distinguishing ovarian cancers from benign gynaecological diseases, particularly endometriosis, and is useful for combination assay or secondary screening for ovarian cancers.