With the high occurrence of genetic anomalies in Brazil and the manifestations of communication disorders associated with these conditions, the development of educative actions that comprise these illnesses can bring unique benefits in the identification and appropriate treatment of these clinical pictures. Objective The aim of this study was to develop and analyze an educational program in genetic syndromes for elementary students applied in two Brazilian states, using an Interactive Tele-education model. Material and Methods The study was carried out in 4 schools: two in the state of São Paulo, Southeast Region, Brazil, and two in the state of Amazonas, North Region, Brazil. Forty-five students, both genders, aged between 13 and 14 years, of the 9th grade of the basic education of both public and private system, were divided into two groups: 21 of São Paulo Group (SPG) and 24 of Amazonas Group (AMG). The educational program lasted about 3 months and was divided into two stages including both classroom and distance activities on genetic syndromes. The classroom activity was carried out separately in each school, with expository lessons, graphs and audiovisual contents. In the activity at a distance the educational content was presented to students by means of the Interactive Tele-education model. In this stage, the students had access a Cybertutor, using the Young Doctor Project methodology. In order to measure the effectiveness of the educational program, the Problem Situation Questionnaire (PSQ) and the Web Site Motivational Analysis Checklist adapted (FPM) were used. Results The program developed was effective for knowledge acquisition in 80% of the groups. FPM showed a high satisfaction index from the participants in relation to the Interactive Tele-education, evaluating the program as "awesome course". No statistically significant differences between the groups regarding type of school or state were observed. Conclusion Thus, the Tele-Education Program can be used as a tool for educational purposes in genetic syndromes of other populations, in several regions of Brazil.