This paper presents results from a study with the following research questions: (a) are pupils’ opinions on genetically modified organisms (GMOs) influenced by biology teaching; and (b) what is important for the opinion pupils hold and how does knowledge work together with other parameters such as values? 64 pupils in an upper secondary school answered questionnaires, in which they expressed opinions and gave arguments on applications of GMOs, before and after biology courses. The pupils’ knowledge of genetics and GMOs was also investigated. Eleven pupils were then interviewed to examine their reasoning in more depth. More pupils were positive about genetically modified tomatoes after the courses. Males were more positive than females. No correlation was found between knowledge of basic genetics and opinion. Most of the pupils could express arguments for and against the applications but they built their personal opinion on different arguments. An important concern was potential risks. Depending on risk judgement and/or how they trusted scientists, the pupils came to different conclusions. Few had any idea of how the different applications are risk assessed or how scientists work. Other important factors for decision-making were the purpose of the application, the time perspective and feelings.