Papillary thyroid cancer (PTC) metastases in the lymph nodes (LNs) were detected by real-time polymerase chain reaction (PCR) for TG and cytokeratin 19 (CK19), and the obtained results were compared with histopathology. 107 LNs from 34 PTC patients were divided into four blocks by a special cutting device - 2 for histopathology, while the other 2 were tested by quantitative real-time PCR. Metastases were detected in 20 nodes from 10 (29.4%) patients. TG and CK19 expression levels differed vastly between nodes with and without metastatic cells. ddCt of TG in the genetic material extracted from N0 nodes was 9.97 ±4.20, while in nodes with metastases ddCt was 0.91±4.20 (p < 0.0001). Cytokeratin 19 showed similar results with expression level (ddCt) in N0 nodes of 10.96 ±2.58 vs. 7.73 ±3.63 in nodes with metastases (p < 0.0001). Evaluation of the utility of both parameters showed efficient differentiation of node involvement in the case of TG, with area under the ROC curve (AUC) equal to 0.91 (95% CI: 0.85-0.96). Cytokeratin 19 also allowed for a degree of differentiation but its diagnostic efficacy was lower (AUC 0.76, 95% CI: 0.64-0.88). The combined TG and CK19 quantitative real-time PCR could be used to select a previously missed group of patients with nodal involvement undetectable by standard histopathology.