Breast cancer accounts for one third of new cancer cases among women. The need for biomarkers for earlydetection is the stimulus to researchers to evaluate altered expression of genes in tumours. Cancer-testis (CT)genes are a group with limited expression in normal tissues except testis but up-regulation in a wide varietyof cancers. We here evaluated expression of two CT genes named FBXO39 and TDRD4 in 32 invasive ductalcarcinoma samples, 10 fibroadenomas and 6 normal breast tissue samples, in addition to two breast cancer celllines, MCF-7 and MDA-MB-231, by the means of quantitative real time RT-PCR. FBXO39 showed significantup-regulation in invasive ductal carcinoma samples in comparison with normal samples. It also was expressedin both cell lines and after RHOXF1 gene knock down it was down-regulated in MCF-7 but up-regulated in theMDA-MB-231 cell line. TDRD4 was not expressed in the MCF-7 cell line and any of the tissue samples excepttestis. However, it was expressed in MDA-MB-231 and was up-regulated after RHOXF1 gene knock down. Ourresults show that FBXO39 but not TDRD4 can be used for cancer detection and if proved to be immunogenic,might be a putative candidate for breast cancer immunotherapy.