We examined selected situational emotions (interest, well-being and anxiety) experienced by 291 secondary school tenth graders during a hands-on gene technology lesson. Two different instruction groups (I-1, I-2) participated in the same teaching unit, in which four basic gene technology experiments were performed. Using a modified "constructivist teaching sequence", a teacher confronted group I-2 with the alternative conceptions of their peers regarding central issues and processes of gene technology in addition to providing the scientific concepts. The pupils within the I-2 group scored higher in the positive emotions of interest and well-being. The negative emotion anxiety was almost absent in both instruction groups. Furthermore, our results indicate a potential influence of interest and well-being upon learning success. Pupils who felt fine and worked with interest in the experimental lessons scored significantly higher on the cognitive achievement test. Eliciting pupils' alternative conceptions and using them in a wide variety of teaching contents is therefore advisable. By doing so, teachers could help create a classroom environment where pupils feel safe and confident. Also, a pupil's interest regarding the choice of material needs to be taken into account if positive emotions need strengthening and the learning achievement needs improvement. (Contains 4 tables and 2 figures.)