Background. Previous studies have evaluated the biomechanical, histological, and clinical effects of rotator cuff repair with different suture materials. However, a histological and western blot analysis after repair comparing nonabsorbable polyester and polyethylene suture materials in a chronic rotator cuff tear model has not been conducted in any previous studies. The aim of this study is to evaluate the effect the two different suture materials, specifically Ethibond and Ultrabraid, have on repair based on a histological evaluation and protein expression by means of a western blot analysis. Methods. Twenty-six rabbits were included in the study. Two rabbits served as normal controls (control group). A bilateral tenotomy of the subscapularis tendon was performed in the remaining 24 rabbits. Six weeks after the tenotomy, the animals were randomly divided into four repair groups (five rabbits in each group) according to the suture material used and the sacrifice time (Ultrabraid two weeks after repair, Ethibond two weeks after repair, Ultrabraid six weeks after repair, and Ethibond six weeks after repair). Two sham-operated groups with two rabbits each were sacrificed at eight and 12 weeks after the tenotomy without repair. Both shoulders of all the animals were used for a western blot (collagen type 1-3, MMP-2, TGF-beta-1, IGF-1, COX-2) analysis and a histological evaluation (fibrocartilage formation, inflammation, vascularisation, collagen density). Results. All groups showed minimal-to-mild histological changes irrespective of the type of suture material used. There was no statistically significant difference in histological scores (p > 0.05). Fibrocartilage formation was greater at six weeks in the polyester suture repair groups without statistical significance (p > 0.05). Collagen type 1-3, MMP-2, TGF-beta-1, IGF-1, and COX-2 were significantly upregulated at two weeks compared to six weeks after repair (p < 0.05). Protein expression levels were statistically significantly higher in the Ultrabraid groups compared to the Ethibond groups (p < 0.05). Conclusions. Changes in the expression of the markers related to rotator cuff healing were demonstrated when repairing with different suture materials, with these being in favour of polyester sutures; however, the histological findings are similar. This finding could influence the design of new suture materials.