We measured the sizes of metastatic lymph nodes and the relationships thereof by (18)F-fluorodeoxyglucose positron emission tomography/computer tomography (PET/CT). We identified risk factors for nodal upstaging in patients with esophageal squamous cell carcinoma (ESCC). Eighty-five patients with ESCC who underwent esophagectomy with extensive mediastinal lymphadenectomy were assessed. Two radiologists blinded to pathology data reviewed PET/CT scans, evaluating both primary tumors and lymph node involvement. A pathologist examined all metastatic lymph nodes in terms of maximal diameter (LNmax), the size of the metastatic focus (Fmax), and the metastasis occupation ratio (MOR = Fmax/LNmax). The maximal tumor length averaged 2.9 ± 0.2 cm and the mean SUVmax of the primary lesion 5.3 ± 0.5. On PET/CT scans, 26 (30.6 %) patients exhibited nodal metastasis and 59 (69.4 %) did not. Pathology grades of pN0, pN1, pN2, and pN3 were assigned to 45 (52.9 %), 24 (28.2 %), 13 (15.3 %), and 3 (3.5 %) patients, respectively. Nodal upstaging was evident in 29 (34.1 %) cases. In 123 metastatic nodes of 4212 nodes dissected, the LNmax was 6.60 ± 0.39 mm, the Fmax 4.47 ± 0.35 mm, and the MOR 0.68 ± 0.03. Of 123 nodes, 85 (69.1 %) were retrieved from PET-negative stations, and the LNmax and Fmax values of these nodes were 5.88 ± 0.42 and 3.75 ± 0.31 mm, respectively. Upon multivariate analysis, tumor length (OR 1.666, p = 0.019) and lymphovascular invasion (OR 41.038, p < 0.001) were risk factors for nodal upstaging. A significant proportion of nodal metastases were too small to detect via PET/CT imaging. Therefore, meticulous lymph node dissection might be helpful in ESCC patients.