The objective of the article is to present the results of an investigation carried out on the basis of the registration of complaints of discrimination based on sexual orientation in the Chilean school system between 2009 and 2015. The cadastre of this information, coming from all the regions of the country, was prepared by the Ministry of Education of Chile (MINEDUC). From that cadastre specific complaints were extracted regarding homophobic discrimination. The sample consisted of 95 cases, of which 61.5% corresponded to female individuals and 38.4% to male individuals. The methodology used prioritized the qualitative analysis, following the assumptions of the Grounded Theory. The textual analysis was made with reference to the notes written by the MINEDUC official who accepted the complaint, which were preserved in their original form, without changing any expressions and emphasis given to the discourse. The results are presented through two axial encodings, one referring to the causes that motivated the discrimination in the denounced institutions and the second to the psycho-emotional, social and pedagogical effects that this discrimination caused in the victims. In the selective coding, the constitutive elements of the homophobic discrimination present in the Chilean school system in the period under study were characterized. The main findings of the investigation show that the grounds for the allegations were motivated by disciplinary measures taken by educational establishments, considered arbitrary by the complainants. Measures aimed at suppressing and punishing LGBT students with sexual dissent, with the consequent reinforcement of school homophobia.