Adenomyosis and endometriosis have a similar pathogenesis; indeed, adenomyosis has been considered by some as a variant of endometriosis ('internal endometriosis'). This study aimed to detect differences in mitochondrial proteins in eutopic endometrial samples from women with adenomyosis (n = 13) and endometriosis (n = 24), and from control patients (n = 29) using surface-enhanced laser desorption/ionization time-of-flight mass spectrometry (SELDI-TOF-MS) protein chip technology. A total of 82 and 78 mitochondrial protein peaks were found in adenomyosis and endometriosis individuals, respectively. Of these, 14 were common to women with adenomyosis and women with endometriosis, although only one of these (mass-to-charge [m/z] ratio 3499) was significantly different between the adenomyosis and endometriosis groups. It is concluded that, compared with control patients, there are differences in the mitochondrial proteins isolated from the eutopic endometrium of patients with adenomyosis and those with endometriosis. Although the changes in mitochondrial proteins in eutopic endometrium from patients with adenomyosis and endometriosis were largely similar, significant differences were also detected. Further identification of these proteins and elucidation of the differences will help towards the differential diagnosis of adenomyosis and endometriosis and new therapeutic approaches.