Purpose: Turner syndrome is defined as total or partial loss of the second sex chromosome in a phenotypically female patient. Due to the possibility of hidden mosaicism of fragments of the Y chromosome and development of gonadoblastoma, we evaluated the presence of such fragments in 2 tissues with different embryonic origins, peripheral blood lymphocytes (mesoderm), and oral mucosal cells (ectoderm) using multiplex polymerase chain reaction. Methods: DNA samples were collected from 109 patients, and primers for the SRY, TSPY, and AMELX genes were used. Results: We found 14 patients (12.8%) with positive molecular markers for the Y chromosome. The study of tissues of different embryological origin showed the same degree of agreement, sensitivity, and specificity. Conclusion Oral mucosa cells have a simpler method of collection that is less invasive and requires less time for DNA extraction at a lower cost.