The regenerative medicine in animals is a rapidly growing field, especially when therapies with stem cells are applied. Currently, stem cells are used for treatment of orthopedic diseases occurring both in small and large animals. Non-steroidal anti-inflammatory drugs (NSAIDs) are routinely used and are often accompanied with adipose derived mesenchymal stem cells (ADMSCs) therapy. Therefore, it is reasonable to monitor morphology of cells and the proliferation status of canine and equine ADMSCs cultured with NSAIDs. We focused on the analysis of the above mentioned parameters. Morphology of investigated cells was monitored using an epifluorescence microscope and scanning electron microscope (SEM). Moreover, SEM analysis was carried out for determination of microvesicles secretion. Proliferation activity of AdMSCs was evaluated with a resazurin-based test. Our research showed that the lowest concentration of Flunixin meglumine (0.01 mg/ml) had a stimulating effect on canine AdMSCs proliferation, while the same concentration significantly slowed down equine stem cell growth. Interestingly, the 0.01 mg/ml concentration of Flunixin meglumine did not effect morphology of the investigated stem cells population. Thus, results obtained from multilevel research allow us to conclude that the lowest concentration of Flunixin meglumine may be accompanied with canine adipose derived mesenchymal stem cells in orthopedic treatment.