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Background: Despite weak evidence, antibiotic prophylaxis prior to endoscopic ultrasound-guided through-the-needle biopsy (EUS-TTNB) of pancreatic cystic lesions (PCLs) is routinely used in clinical practice. We aim to compare a group of patients treated with antibiotics before EUS-TTNB of PCLs and a group who did not undergo antimicrobial prophylaxis. Methods: Out of 236 patients with pancreatic cystic lesions referred to two high-volume centers between 2016 and 2021, after propensity score matching, two groups were compared: 98 subjects who underwent EUS-TTNB under antibiotic prophylaxis and 49 subjects without prophylaxis. Results: There was no difference in terms of baseline parameters between groups. Final diagnosis was serous cystadenoma in 36.7% of patients in the group not treated with prophylaxis and in 37.7% of patients in the control group, whereas IPMN and mucinous cystadenoma were diagnosed in 3 (6.1%) and 16 (32.6%) versus 6 (6.1%) and 32 (32.6%) patients in the two groups, respectively (p = 0.23). Overall, the adverse event rate was 6.1% in the group not treated with antibiotic prophylaxis and 5.1% in the control group (p = 0.49). Only a single infectious adverse event occurred in each group (p = 0.48). The diagnostic yields were 89.7% and 90.8% in the two groups (p = 0.7), and the diagnostic accuracy rate was 81.6% in both groups (p = 1.0). Conclusions: Prophylactic antibiotics do not seem to influence the risk of infection, and their routine use should be discouraged.