Summary During surgery for thoracic esophageal cancer, the resected esophagus remains in the thoracic cavity, allowing fluid to leak from the specimen. If this fluid contains cancer cells, they may spread throughout the cavity. However, the presence and prognostic impact of free cancer cells in leaked fluid from the esophagus (LF-E) remain unclear. We conducted a prospective cohort study of 96 patients with thoracic esophageal cancer who underwent radical subtotal esophagectomy. After the thoracic procedure, the esophagus was placed in a bag and removed following the abdominal and cervical procedures. Fluid collected from the bag, combined with saline used to rinse the specimen, was defined as LF-E and examined cytologically. We evaluated the clinicopathological characteristics and prognosis of LF-E-positive (LF-E [+]) patients. LF-E (+) was observed in 5 of 96 patients (5.2%), all of whom had pT3 or higher squamous cell carcinoma with nodal metastasis and vascular invasion. Among the 44 patients with pT3-4a disease, those in the LF-E (+) group had significantly poorer regression-free survival (RFS) (P < 0.001) and overall survival (OS) (P < 0.001) than those in the LF-E-negative group. Multivariate Cox regression analysis identified LF-E positivity as an independent prognostic factor for RFS (hazard ratio [HR]: 4.57, 95% confidence interval [CI]: 1.21–16.2, P = 0.026) and OS (HR: 11.9, 95% CI: 2.04–69.1, P = 0.008). The presence of free cancer cells in LF-E indicated a poor prognosis in patients with pT3 or higher esophageal cancer. LF-E positivity may serve as a new prognostic biomarker.