Background: In a previous work, we identified nine founder mutations present in close to 80% of BRCA1 and BRCA2 mutation carriers, and distributed across the country. The presence of founder mutations constitutes a valuable opportunity to develop new strategies for genetic screening. Genetic tests are primarily performed by NGS sequencing, which requires sophisticated and expensive equipment, and it takes 2–3 weeks for the results to be informed to the patient. In addition, genetic tests are not covered by insurance companies in Latin American countries. In this work, we present the standardization and technical validation of a real-time PCR based methodology for allelic discrimination in order to identify the nine Chilean founder mutations in BRCA1 and BRCA2 genes. Methods and results: We designed nine pairs of probes and nine pairs of primers to amplify synchronically nine regions of the BRCA1/BRCA2 genes by real-time PCR, in order to identify the nine founder mutations through allelic discrimination analyses. Technical validation was performed using 90 positive and 90 negative samples for each mutation. The methodology was tested in a second group of 60 patients. Our method correctly classified carriers and non-carriers of one of the nine Chilean founder mutations with a 100% specificity and 100% sensitivity, compared with Sanger sequencing performance. Conclusions: We develop an inexpensive, simple, and fast mutation detection method that could be implemented locally in Hospitals from the Private to Public health system. This methodology may be useful for the screening of BRCA1 and BRCA2 mutations in other populations.