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Introduction: Circulating tumor cells (CTCs) have the characteristics of cancer stem cells and play an important role in the recurrence and metastasis of tumors. CD44 is a surface marker molecule for gastric cancer stem cells (GCSCs) and can be used to identify and isolate GCSCs. Here, we investigated the effect of CD44 protein expression, circulating tumor cells, and CD44-positive CTCs on the prognosis of gastric cancer (GC)., Material and Methods: Blood samples from 58 GC patients being treated at the First Affiliated Hospital of Anhui Medical University from August 2015 to October 2016 were obtained before surgery. The cancer tissues from 58 GC patients after surgery and the same amount of adjacent normal tissues 5 cm away from the center of the cancer tissues were collected as controls. Immunohistochemistry was used to detect CD44 expression in cancer tissues and adjacent normal tissues. Immunomagnetically negative enrichment combined with im-FISH was used to detect CTCs and CD44-positive CTCs in gastric cancer patients., Results: Circulating tumor cells were detected in 44 of 58 patients, and CD44 protein was positive in 34 cases of GC. The presence of CTCs and CD44 is significantly associated with depth of tumor infiltration, lymph node metastasis, TNM stage, and recurrence ( p < 0.01). Twenty-nine of 44 CTC-positive patients had CD44-positive CTCs. The patients with CD44-positive CTCs were more likely to develop recurrence than patients with CD44-negative CTCs ( p < 0.01). Furthermore, 28 of 29 patients with CD44-positive CTCs developed recurrent disease, and the mean time to recurrence was shorter than that in patients with CD44-negative CTCs (16.030 ±5.268 and 21.800 ±4.601 months; p < 0.01). The Cox proportional hazards model indicated that the presence of CD44-positive CTCs and TNM stage were independent predictors of recurrence for GC ( p = 0.044 and 0.035)., Conclusions: The detection of stem cell characteristics of GC CTCs can provide more prognostic information than simply detecting GC CTCs and GC CD44 expression., Competing Interests: The authors declare no conflict of interest., (Copyright: © 2020 Termedia & Banach.)