Background: Polycystic ovary syndrome (PCOS) has an unknown and complex etiology. It affects 5–10% of women in the reproductive age. Patients are known to have increased ovarian androgen production that is associated with decreased menses, hirsutism, and acne. Urinary tract stones (UTS) are a multifactorial disorder, with age and sex being known risk factors. Many PCOS patients are obese, and links between nephrolithiasis and obesity have been shown previously. Objectives: To identify the relation between PCOS and UTS considering the patients' body mass index (BMI). Methods: This is a cross-sectional study that enrolled 407 women aged 18-40 who attended the gynecology and obstetrics clinic at Al-Elwiya Maternity Teaching Hospital. The patients were assigned to the PCOS group or the control group. The data collected includes age, weight, height, body mass index (BMI), and the results of abdominal ultrasonography to detect UTS. Results: One hundred ninety women were in the PCOS group and 217 in the control group. The PCOS group had a higher BMI than the control group. Patients with UTS had a higher BMI than those without UTS. PCOS combined with a higher BMI showed an increased risk of having UTS. However, analysis of each of the variables taking the other into account showed no significant association. Conclusions: PCOS and BMI both raise the chances of having UTS; however, each one showed no significant association when adjusting for the other.