Introdution: The morphological characteristics obtained by craniometry may be the key to sex determination and enable us to identify unknown individuals in anywhere in the world. Aims: The purpose of this study was to evaluate the effectiveness of the linear morphometry of foramen magnum to verify the morphological characteristics for gender determination in human skulls of Brazilian individuals. Methods: With a digital caliper, were made three non-consecutive measurements of the foramen magnum in 215 human skulls (139 male and 76 female), from the collection of the Department of Morphology and Descriptive Topography – UNIFESP/SP with registered data on nationality, gender, and age. The craniometric measurements were made in accordance with the protocol defined by Günay and Altinkök (2000). The data were submitted to intraclass correlation coefficient (ICC) and Student t-test with significance level of 5%. Results: There were no statistically significant differences (chi-square, p > 0.05) between the ethnic groups within each gender. The ANOVA and Tukey tests showed that the gender influenced the width of the foramen magnum. The FM is higher in males (30.3 ± 0.20) than in females (29.4 ± 0.23), but not in length (p < 0.05). Conclusion: The morphometric linear method of the foramen magnum (width) was able to determine the morphological differences between sexes and can be used in conjunction with other anthropological techniques to gender determination of unknown individuals.