Mesenchymal stem cells (MSCs) are useful for various purposes, including tissue engineering, regeneration, and gene therapy. MSCs isolated from extraocular muscles (EOMs) can be easily expanded in vitro, and can undergo multilineage differentiations involving adipogenesis, chondrogenesis, osteogenesis, and even neuronal or myogenic differentiation. This study aimed to isolate, characterize, and compare extraocular muscle-derived muscle progenitor cells (EOM-MPCs) from normal subjects and patients with Graves' orbitopathy (GO). EOM was obtained during strabismus surgery. Flow cytometry was conducted to identify CD surface antigens such as CD34, CD45, CD44, CD59, CD73, and CD90. We quantitated various cytokines secreted from MSCs, including interleukin (IL)-1a, IL-2, IL-6, IL-8, IL-10, IL-12, IL17A, tumor necrosis factor (TNF)-a, and interferon (IFN)-g, using a multi-analysis enzyme-linked immunosorbent assay array kit. We performed Oil Red O staining for adipogenesis, Alzarin Red staining for osteogenesis, Alcian blue staining for chondrogenesis, and polymerase chain reaction to measure messenger RNA expression during myogenesis. Our results show that EOM-MPCs from normal subjects and GO patients had similar levels of surface antigen expression and cytokine secretion. There was also no significant difference in the multilineage differentiation of adipocytes, chondrocytes, osteocytes, and myoblasts from EOM-MPCs taken from normal subjects and GO patients. However, hyaluronic acid synthetase 2 expression was higher after induction with tafluprost in EOM-MPCs from GO patients when compared with normal subjects. Together, these results show that EOM-MPCs derived from normal subjects are a good source for stem cell-based therapy for various disorders.