Breast cancer is the most frequent cancer among women in Slovenia. Male breast cancer, however, is a rare disease comprising less than 1% of breast cancer patients in Slovenia. The causes for some of inherited cases are mutations of the BRCA1 or BRCA2 genes. BRCA2 gene mutation carriers have an increased risk of breast cancer. It is estimated that 15% of men who carry a germ-line BRCA2 gene mutation will develop breast cancer. Studies in various countries have shown varying frequencies of BRCA2 gene mutations. There is no information about the frequency of mutation carriers in the Slovene male breast cancer population. The purpose of our population-based study was to determine the frequency of BRCA2 or BRCA1 gene mutation carriers among male breast cancer patients in Slovenia. Our study hypothesis was: The frequency of BRCA2 gene mutation carriers among male breast cancer cases is over 10%. Records on 136 male patients treated for breast cancer between 1975 and 2005 at the Ljubljana Institute of Oncology were retrieved. At the time of our study, 38 of those patients were still alive. They were invited to receive genetic counselling and undergo genetic testing. Genetic testing was performed using blood samples at the Laboratory of Oncological Genetics at the Vrije Universiteit in Brussels. The BRCA1 and BRCA2 genes were screened for mutations using the PTT and F-CSGE tests, then the high peaked samples were sequenced. Twenty-two male breast cancer patients were tested. BRCA2 gene mutation was identified in three male breast cancer patients. Two of them carried the Slovene founder mutation IVS16-2a > G. This mutation has been found in nine Slovene families so far. None of our patients had BRCA1 mutation. The median age of all our patients with breast cancer was 58 years (range 17 to 86 years). The median age of the patients with BRCA2 gene mutation was 64 years and of those without mutation it was 57 years. There was no statistical difference in the ages of the patients with mutation and those without it (p = 0.41). There was also no statistical difference in the stage of disease in patients with mutation and those without it (p = 0.21). The frequency of BRCA2 gene mutations among male breast cancer patients in Slovenia is 14%.