Introduction: In recent years, various subspecies of Mycobacterium intracellulare have been identified. However, there are still limited reports on the clinical characteristics of each subspecies. In this study, we examined the clinical characteristics of three subspecies of M. intracellulare: M. intracellulare subsp. intracellulare, M. intracellulare subsp. paraintracellulare, and M. intracellulare subsp. chimaera. Methods: We performed genomic analysis on strains stored in our hospital from 2015 to 2021 and reviewed medical records of patients. The primary endpoints were unfavorable outcomes such as smear-positive conversions, worsening imaging findings, hospitalization, and death. Results: A total of 128 patients were screened, and 91 patients met the ATS/ERS/ESCMID/IDSA Clinical Practice Guideline diagnostic criteria. Patients with less than six months of follow-up were excluded, and 61 patients were included in the analysis. Of these, 22 had subsp. intracellulare, 29 had subsp. paraintracellulare, and 10 had subsp. chimaera. The median age of each group was 71.5/ 73/ 66.5 years, and the proportion of patients over 60 years old was similar among the three groups. Although there were fewer women in M. chimaera group, there were no significant differences in BMI, underlying diseases,or smoking history. Furthermore, there were also no significant differences in the cumulative incidence of unfavorable outcomes. Conclusion: Our study found no significant differences in the clinical background or clinical course among the three subspecies of M. intracellulare. However, larger studies are needed to further examine the clinical characteristics of each subspecies.