Previous studies on the factorial structure of the Patient Health Questionnaire (PHQ-9) have yielded divergent results, and there is no consensus on which factorial structure provides a more adequate fit. In Colombia, no precise method to estimate the factorial structure of the PHQ-9 has been used. The purpose of this study is to evaluate the factorial structure of the PHQ-9 as a depression screening tool in university students of Colombia from a model of two factors previously studied. The PHQ-9 was applied to 550 health science university students. A factorial confirmatory analysis was carried out using a structural equations model and invariance analysis. The model with one somatic factor and one non-somatic factor, achieved a better fit with invariance by gender. The PHQ-9 used as a depression screening tool used in university students in Cartagena revealed two factors, one somatic and one non-somatic with measurement invariance by gender.