Analysis of genetic predisposition to cancer provides valuable information for early cancer detection or even prevention. The 5382insC insertion in the BRCA1 gene is the most frequent mutation among those associated with high breast cancer risk in women of East European origin. A method for 5382insC detection with fluorescent labeled allele-specific oligonucleotides in the Duplex Scorpion format has been developed. The method can be used under real-time PCR conditions as well as under the conditions of end-point fluorescence measurement following regular PCR. The adequacy of the method was demonstrated in the study of the 5382insC mutation frequency in breast cancer patients. A total of 564 genomic DNA samples from breast cancer patients were screened. Eleven patients (1.95%) were found to carry the mutation under consideration in the heterozygous state. The 5382insC allele frequency in the breast cancer patient group was 0.0098. The method is appropriate in clinical practice to detect individuals at high breast cancer risk, as well as in large-scale population studies.