Objective To investigate the prognostic influence of DNA ploidy and S-phase fraction (SPF) on disease-free (DFS) and overall survival (OS) of patients with primary disease and loco-regional lymph node recurrence of papillary thyroid carcinoma (PTC). Design A large prospective study with long-term follow-up (median, 117 similar to months). Patients Two series of patients with primary PTC (n similar to=similar to 305) and lymph node recurrence metastasis (LNM) (n similar to=similar to 39) were involved in the study. Measurements Patient's age and gender, histological variant, pathological tumour-node-metastasis (pTNM) staging, extrathyroidal extension, vascular and lymphatic invasion and tumour bilateral growth were the clinical and pathological characteristics evaluated. DNA flow cytometry was performed on fresh/frozen surgical tumour samples. Cox regression models were estimated for prognostic analyses. Results Seventeen (5.6%) primary tumours and five (12.8%) LNMs were aneuploid, while mean SPF was 2.7% and 3.7%, respectively (P similar to=similar to 0.022). High SPF was significantly associated with lymphatic invasion and tall cell and diffuse sclerosing variants. In univariate analysis, all the clinico-pathological variables, but tumour bilateral growth and gender, were significantly correlated with survival. SPF showed borderline significance (P similar to=similar to 0.051) in relation to OS. In multivariate analysis, older age (=48 similar to years), lymph node spread and high SPF were significantly adverse prognostic factors. Extrathyroidal extension and distant metastasis for OS, as well as tumour size for DFS, were also found as unfavourable prognostic features. In LNM, the KaplanMeier curves showed significant differences for older age and DNA aneuploidy (recurrence; P similar to=similar to 0.011). Conclusion The results indicate that SPF and ploidy can provide additional predictive information in patients with PTC.