In many higher education curricula, pre-structured step-by-step laboratory exercises in introductory courses in geographical information systems (GIS) are an important part of the training of future geographers. The reasons for this approach to teaching GIS are manifold, such as large numbers of students, off-the-shelf desktop software that is often complex, technical challenges, and scarce faculty resources. Often the reasons are well agreed upon by members of a university faculty and among the students. Research in other fields has shown that the use of a controlled manual for laboratory work often provides low learning potentials. However, not much empirical research has dealt with this issue within a GIS learning environment. Inspired by research on the value of student-generated questions within science education, the authors take a closer look at the type of student-generated questions and their relation to students' self-image of their learning approach in two pre-structured GIS laboratory settings at two Danish universities. They conclude that the vast majority of student-generated questions are of a basic information type and independent of the students' self-image of their learning approach. Further, it is found that wonderment questions, i.e. questions that are reflective in nature and show students the process towards acquiring extended geographical knowledge and software proficiency, are rarely asked.