To investigate the ability of matrix metalloproteinase (MMP)-2 and CD44 variant 6 (CD44v6) protein levels to diagnose papillary thyroid cancer (PTC), compared with routine diagnostic methods using tissue sections; to explore the relationship between MMP-2 and CD44v6 protein levels and lymph node metastases (LNM) in PTC. Archival PTC specimens from patients with PTC, with or without lateral cervical LNM, were included in this retrospective immunohistochemical study. MMP-2 and CD44v6 protein levels were analysed immunohistochemically using routinely prepared tissue sections. Specimens from 66 patients with PTC were reviewed retrospectively (35 patients with lateral cervical LNM; 31 patients without LNM). The percentages of samples with cells that demonstrated positive protein staining differed significantly between PTC specimens, benign thyroid nodules and adjacent normal follicular epithelium (MMP-2: 86.4%, 60.0%, and 25.7%, respectively; CD44v6: 80.3%, 37.1% and 22.9%, respectively). The level of CD44v6 protein staining was found to be significantly and positively correlated with the level of MMP-2 protein staining in PTC specimens. Both MMP-2 and CD44v6 might be useful tumour markers for predicting risk of lateral cervical LNM in patients with PTC.