Oligofructose prebiotic fiber supplementation has been reported to mitigate the effects of a high fat/high sucrose diet and reduce knee joint degeneration in male rats. However, few studies investigated the development of osteoarthritis and bone lesions as a function of sex and in joints other than the knee. This study was aimed at to quantifying the effect of a HFS diet and prebiotic fiber supplementation on shoulder joint health in male and female Sprague-Dawley rats. Rats were randomized into 6 groups: 2 groups fed a chow diet: Chow-Male n = 11, Chow-female n = 12; 2 groups fed a HFS diet: HFS-Male n = 11, HFS-Female n = 12; and 2 groups fed a prebiotic fiber supplement in addition to the HFS diet: Fiber-Male n = 6, Fiber- Female n = 12. After 12 weeks, shoulder joints were histologically assessed for OA. Body composition, serum lipid profile, insulin resistance and fecal microbiota were also assessed. Shoulders in male and female rats appear to be protected against degeneration when exposed to a HFS diet. Male rats developed bone lesions while females did not. Fiber supplementation was more effective in males than in females suggesting that fiber supplementation may have sex-specific effects on the gut microbiota.