The objective of the study was to demonstrate the effect of concentrated bone marrow stem cells (MSCs) to the healing of sutured tendon of the supraspinatus muscle in comparison to the same procedure performed without MSCs. We have postulated the hypothesis that MSCs enhance the healing of the sutured supraspinatus tendon to its humeral footprint. Methods and findings: None of the patients had to be excluded from our prospective randomized study. 50 patients met the indication criteria for isolated supraspinatus surgery. 25 patients (Group I) received MSCs into the supraspinatus footprint. 25 patients (Group II) was treated without the use of MSCs. Patients were examined pre-operatively, 6, 12 and 24 months after the surgery and assessment included physical examination, visual analogue scale (VAS), ASES (American Shoulder and Elbow Surgeons Standardized Shoulder Assessment Form) and Constant score. Patients underwent MRI 2 years postoperatively. Findings were compared with the preoperative results. We have found no statistically significant differences between both groups pre-operatively. After a 24-month follow-up period there were significant differences observed in all clinical outcomes. When compared results between both groups two years postoperatively, p-value (p=0.05) for the VAS score was 0.0176 and for the Constant score 0.0355. The only statistically non-significant was p-value for the ASES score comparing results from both groups at two years follow-up (p=0.085). The MRI findings at 2 years showed fully healed tissue of the rotator cuff tendon in 17 patients in the Group I, but only in 9 patients in the Group II. Conclusions: We have accepted the hypothesis that MSCs enhance the healing of the sutured supraspinatus tendon to its humeral footprint.