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Background: Primary dysmenorrhea is one of the most common gynecological complaints that can affect the quality of life. The exact pathophysiology of dysmenorrhea is not yet fully understood. However, some studies have suggested an association between anthropometric indices and dysmenorrhea. Objectives: We aimed to evaluated the association between anthropometric indices and dysmenorrhea. Methods: In this cross-sectional study conducted in Qazvin, Iran, during 2016, 400 high school students aged between 14 and 18 years old were enrolled based on the inclusion criteria. The relevant information and anthropometric indices were collected using a checklist. The data were analyzed by SPSS version 17. Results: Among 400 students, the prevalence of dysmenorrhea was 82.5%. There were significant differences in cycle length (29.15 ± 2.69 vs. 27.57 ± 2.38; P = 0.001), duration of menstruation (6.03 ± 1.11 vs. 5.65 ± 1.20; P = 0.011), hip circumference (93.13 ± 9.25 vs. 90.14 ± 12.15; P = 0.021), height (162.62 ± 5.47 vs. 160.72 ± 5.92; P = 0.01), and waist to hip ratio (WHR) (0.78 ± 0.06 vs. 0.81 ± 0.09; P = 0.001) between the groups with dysmenorrhea and without dysmenorrhea. Based on a logistic regression model, only WHR was a predictive protective factor for dysmenorrhea (OR = 0.896, CI95% = 0.821 - 0.971, P = 0.012) and height (OR = 1.057, CI95% = 1.006 - 1.111, P < 0.001), cycle length (OR = 1.238, CI95% = 1.117 - 1.372, P = 0.028), and menstruation length (OR = 1.269, CI95% = 1.002 - 1.608, P = 0.048) were risk factors. Conclusions: WHR and height were noted to be associated with dysmenorrhea. In addition, WHR was found to be a protective factor and height to be a risk factor.