We used morphoproteomics to investigate mammalian target of rapamycin (MTOR) signaling pathway in papillary thyroid carcinomas and correlated the results with clinicopathological parameters. Archival paraffin-embedded tissue of papillary thyroid carcinomas was obtained from 30 patients, including 15 classical type and 8 follicular, 4 tall-cell, 1 columnar-cell, 1 diffuse sclerosing and 1 cribriform variants. Immunohistochemical stains were performed for three phosphorylated (p) protein analytes: p-MTOR (Ser2448), p-Akt (Ser473) and p-p70S6K (Thr389). Chromogenic signals and subcellular compartmentalization (nuclear, cytoplasmic and plasmalemmal) were evaluated. Clinicopathological parameters were reviewed. Immunoreactivities for p-MTOR, p-Akt and p-p70S6K were observed in all papillary thyroid carcinomas. In addition to an expression of p-MTOR in cytoplasmic location, nuclear translocation of p-MTOR with variable loss of plasmalemmal expression, and with concomitant nuclear expression of p-Akt, was also identified in all tall-cell, columnar-cell and diffuse sclerosing variants of papillary thyroid carcinoma. There were no significant differences in the clinicopathological parameters, including tumor size, extrathyroidal extension, angioinvasion and nodal metastases between the groups with and without nuclear expression of p-MTOR (P>0.05). The expressions of p-MTOR in cytoplasmic and/or plasmalemmal locations with the concomitant immunoreactivity for p-p70S6K in all papillary thyroid carcinomas indicate the activation of MTOR complex 1 pathway. The nuclear translocation of p-MTOR evidences the activation of MTOR complex 2 and is identified only in the known aggressive histological variants of papillary thyroid carcinoma, including tall-cell, columnar-cell and diffuse sclerosing variants. Thus, these results suggest the constitutive activation of MTOR signaling pathway in papillary thyroid carcinomas and provide a new insight of biogenetic basis for the aggressive histological variants of papillary thyroid carcinoma. The pattern of expression of p-MTOR in papillary thyroid carcinomas may serve as a diagnostic/prognostic marker and a potential therapeutic target.