The purpose of this study is to investigate the students’ attitudes towards science and religion in the Portuguese Secondary Education. The sample consists of 308 students (110 males and 198 females), including 200 Catholics and 49 atheists, from two Portuguese schools (one private and one public). A questionnaire, based on previous instruments [1] [2] and on new items, was used. An exploratory factor analysis was conducted. For the first part of the questionnaire [1] eight factors were retained, including items associated with (i) faith; (ii) scientists; (iii) perspectives of science on religion; (iv) science and religion classes; (v) laws of nature; (vi) trust in science; (vii) interest in science and religion dialogue; (viii) scientific proof of the existence of God. Students expressed great confidence on science and reported to accept science theories on evolution and world beginning. Students do not perceive science classes/teachers neither religion classes/teachers to ignore their religious faith. The answers to the second part of the questionnaire [2] indicated that students acknowledge that science and religion teachings often enter in conflict and, accordingly, they are not completely, compatible. Students think that scientists should be free to investigate without any interference and statistical significant differences were found between Catholics and atheists. Although the new items need further work and revision, they indicated that the source of the tension between science and religion is not in the Bible nor in the evolution theory. The current findings suggest that creationism might not be as relevant for science and religion dialogue in the Portuguese context as it might be in America or England and that the scientific perspective is dominant in many regards. Ethics may be an important avenue to link science and religion, but it remains unclear what the nature of religion is and how it affects students in their relation with science. Future studies must include a larger sample of students from Secondary Education public schools in order to understand the significance of these preliminary results and to clarify where the source of tension between science and religion lays