Objectives: The superiority of EUS-guided fine-needle biopsy (EUS-FNB) over fine-needle aspiration (FNA) remains controversial. This study aimed to compare the efficacy of FNB and FNA in immunohistochemistry (IHC)-required lesions, including, type 1 autoimmune pancreatitis (AIP), neuroendocrine tumor (NET), mesenchymal tumor, and lymphoma.Methods: In this multicenter study, specimens from all eligible patients who underwent EUS-FNB/FNA with these specific lesions were prospectively evaluated. Demographics, adequacy of specimens for IHC, diagnostic accuracy, and integrity of tissue were analyzed. Subgroup analysis and multivariate logistic regression were also performed to control confounders.Results: A total of 439 patients were included for analysis. Most lesion types were type 1 AIP (41.69%), followed by NET, mesenchymal tumor, and lymphoma. FNB yielded specimens with better adequacy for IHC (82.41% vs. 66.67%, P < 0.001) and higher diagnostic accuracy (74.37% vs. 55.42%, P < 0.001). The superiority of FNB over FNA in adequacy for IHC (odds ratio, 2.786 [1.515-5.291]) and diagnostic accuracy (odds ratio, 2.793 [1.645-4.808]) remained significant after control of confounders including needle size, lesion site, lesion size, and endoscopists. In subgroup analysis, FNB showed higher diagnostic accuracy in AIP and mesenchymal tumor, whereas no statistically significant difference was observed in NET and lymphoma.Conclusions: FNB was superior to FNA needles in obtaining tissues with better adequacy and integrity. These results suggest that FNB should be considered a first-line modality in the diagnosis of IHC-required lesions, especially AIP and mesenchymal tumor. However, a randomized controlled trial with larger sample size is needed to further confirm our findings.