Methods of assessing the immunomodulatory potential of a multipotent stromal cell (MSC) population are provided. Aspects of the methods include evaluating the amount of CD54/IL-6 associated with an MSC in a sample of the MSC population to obtain a CD54/IL-6 result and providing an assessment of the immunomodulatory potential of the MSC population based on the obtained CD54/IL-6 result. Also provided are systems and kits that find use in practicing the subject methods.