Interstitial lung disease (ILD) is a serious complication of connective tissue diseases (CTDs). The heterogeneity of ILDs reflects differences in pathogenesis among diseases. This study aimed to clarify the characteristics of CTD-ILDs via a detailed analysis of the bronchoalveolar lavage fluid (BALF) and blood immune cells. BALF and blood samples were collected from 39 Japanese patients with newly diagnosed ILD: five patients with Sjögren's syndrome (SS), eight patients with dermatomyositis (DM), six patients with rheumatoid arthritis (RA), six patients with systemic sclerosis, four patients with anti-neutrophil cytoplasmic antibody-associated vasculitis, and 10 patients with idiopathic interstitial pneumonia. We performed single-cell RNA sequencing to analyze the gene expression profiles in these patients' immune cells. In patients with SS, B cells in the BALF were increased and genes associated with the innate and acquired immunity were enriched in both the BALF and blood. In contrast, patients with DM showed an upregulation of genes associated with viral infection in both the BALF and blood. In patients with RA, neutrophils in the BALF tended to increase, and their gene expression patterns changed towards inflammation. These disease-specific characteristics may help us understand the pathogenesis for each disease and discover potential biomarkers., Competing Interests: Author KB was employed by the company Aimed Analytics GmbH. WF receives fundings from Nippon Boehringer Ingelheim Co., Ltd. and GlaxoSmithKline Consumer Healthcare Japan K.K., grants from Takeda Pharmaceutical Company Limited, and speaking fees from Asahi Kasei Pharma Corporation, Astellas Pharma Inc., Mitsubishi Tanabe Pharma Corporation, and Chugai Pharmaceutical Co., Ltd. TT receives speaking fees from Asahi Kasei Pharma Corporation, Chugai Pharmaceutical Co., Ltd., Nippon Boehringer Ingelheim Co., Ltd., and Novartis Pharma K.K. AO receives speaking fees from AbbVie GK, Chugai Pharmaceutical Co., Ltd., Eisai Co., Ltd., Ono Pharmaceutical Co., Ltd., DAIICHI SANKYO COMPANY, LIMITED, Astellas Pharma Inc., AstraZeneca, Mitsubishi Tanabe Pharma Corporation, Pfizer Japan Inc., Asahi Kasei Pharma Corporation, Novartis Pharma K.K., Gilead Sciences, Inc., Janssen Pharmaceutical K.K., GlaxoSmithKline Consumer Healthcare Japan K.K., and Eli Lilly Japan K.K. TS receives consulting fees from Asahi Kasei Pharma and speaking fees from Asahi Kasei Pharma Corporation, Astellas Pharma Inc., AbbVie GK, GlaxoSmithKline Consumer Healthcare Japan K.K., Mitsubishi Tanabe Pharma Corporation, Chugai Pharmaceutical Co., Ltd., Eli Lilly Japan K.K. Nippon Boehringer Ingelheim Co., Ltd., and Pfizer Japan Inc. MW receives speaking fees from Asahi Kasei Pharma Corporation, Astellas Pharma Inc., AbbVie GK, Gilead Sciences, Inc., GlaxoSmithKline Consumer Healthcare Japan K.K., Mitsubishi Tanabe Pharma Corporation, Chugai Pharmaceutical Co., Ltd., Eli Lilly Japan K.K., and Pfizer Japan Inc. MK receives speaking fees from AbbVie GK, Asahi Kasei Pharma Corporation, Astellas Pharma Inc., GlaxoSmithKline Consumer Healthcare Japan K.K., Mitsubishi Tanabe Pharma Corporation, Chugai Pharmaceutical Co., Eli Lilly Japan K.K., Nippon Boehringer Ingelheim Co., Ltd., and Pfizer Japan Inc. WF receives speaking fees from Asahi Kasei Pharma Corporation, Astellas Pharma Inc., AbbVie GK, Gilead Sciences, Sawai Pharmaceutical Co., Ltd., Mitsubishi Tanabe Pharma Corporation, Chugai Pharmaceutical Co., Ltd., Eli Lilly Japan K.K., and Pfizer Japan Inc. and represents committees supported by Astellas Pharma Inc. and AYUMI Pharmaceutical Corporation. KY receives supports for attending meetings from Shionogi Pharma Co., Ltd. KT receives grants from Chugai-Roche, Boehringer-Ingelheim, Ono Pharmaceutical, and Taiho Pharmaceutical, consulting fees from Ono Pharmaceutical, lecture fees from Eli Lilly, Ono Pharmaceutical, AstraZeneca, Chugai-Roche, Boehringer-Ingelheim, MSD-Merck, and Daiichi-Sankyo, and serves on the board member of Japan Lung Cancer Society. YuK receives grants from Asahi Kasei Pharma Corporation, AbbVie GK, AYUMI Pharmaceutical Corporation., Gilead Sciences, Inc., Mitsubishi Tanabe Pharma Corporation, Chugai Pharmaceutical Co., Ltd., and Nippon Boehringer Ingelheim Co., Ltd. and speaking fees from Asahi Kasei Pharma Corporation, Astellas Pharma Inc., AbbVie GK, AYUMI Pharmaceutical Corporation., GlaxoSmithKline Consumer Healthcare Japan K.K., Mitsubishi Tanabe Pharma Corporation, Chugai Pharmaceutical Co., Nippon Boehringer Ingelheim Co., Ltd., Novartis Pharma K.K. Pfizer Japan Inc., and Mylan Inc. Author KB was employed by the company Aimed Analytics GmbH. The remaining authors declare that the research was conducted in the absence of any commercial or financial relationships that could be construed as a potential conflict of interest., (Copyright © 2024 Hirano, Sakashita, Fujii, Baßler, Tsuji, Kadoya, Omoto, Hiraoka, Imabayashi, Kaneko, Sofue, Maehara, Seno, Wada, Kohno, Fukuda, Yamada, Takayama and Kawahito.)