Objective Adenomyosis and endometriosis are relatively common gynecological diseases that exhibit many common features. This study identified gynecological and non-gynecological diseases that exhibited comorbidity with adenomyosis and endometriosis in Korean women. Methods We used Health Insurance Review and Assessment data from 2009 to 2011 and searched for adenomyosis and endometriosis (coded as N80.1 and D25 in International Classification of Disease, 10th revision [ICD-10], respectively). We selected records from patients who had independent disease occurrences in each year, and comorbidities were estimated using Fisher's exact test. We computed each year's similarities and combined 3 years' results using Fisher's P-value summation method. Results A total of 61,516 patients' data were collected during the study period. The prevalence of adenomyosis and endometriosis were similar each year: 12.4% and 9.3% in 2009, 12.5% and 9.4% in 2010 and 13.3% and 9.1% in 2011, respectively. Meta-analysis revealed that 31 ICD-10 codes were significantly related with adenomyosis, and 44 ICD-10 codes were related with endometriosis. Gynecological diseases, such as leiomyoma and benign ovarian tumor, were significantly related to adenomyosis and endometriosis. Non-gynecological diseases, such as anemia and hypercholesterolemia, were also related to adenomyosis and endometriosis. Conclusion We must monitor for the presence of gynecological and non-gynecological diseases with co-morbidities during evaluations and follow-up of patients with adenomyosis or endometriosis.