Background: Polycystic ovary syndrome (PCOS) is one of the most common endocrinopathies in women of childbearing age. As a complex structure, the extracellular matrix (ECM) and its components, including glycosaminoglycans (GAGs) and collagens, are highly affected by hormonal alterations. Objectives: This study aimed to evaluate the level of GAG and hydroxyproline in the follicular fluid (FF) of women with PCOS. Methods: Overall, 62 women referring to Fatemieh Hospital Infertility Center in Hamadan were evaluated in this study. FF samples were taken from 31 women with PCOS during ovarian puncture and 31 healthy women. Oocytes were evaluated in the different stages of maturation, namely, metaphase II (MII) and germinal vesicle (GV). Commercially available kits were used to measure the levels of glycosaminoglycans and hydroxyproline. Results: The results of the present study showed that the count of oocytes in women with PCOS was significantly higher than that in healthy women. Evaluating GAG and hydroxyproline levels indicated that their levels were meaningfully higher in the FF of women with PCOS. Conclusion: In general, the results of this study suggested that ECM changes in PCOS followed by alterations in the levels of GAGs and hydroxyproline may lead to an increase in the level of GAG and hydroxyproline in the FF. The evaluation of these markers may be the subject of further studies.