The aim of this study is to explore the development of experimental skills of students that are actively involved in virtual object manipulations in a virtual laboratory environment. We particularly investigate the development of their design of experiment skills. The study refers to 14 students of a lower secondary school in Greece and their development was tested by applying a pre-post comparison methodology in written tests and personal interviews. Students attended a teaching course about thermal phenomena witch had two innovative characteristics: the active engagement of the students in laboratory activities and the extensive use of ICT. Students’ development was tested in 5 dimensions of their experiments’ design and our findings support that after the course, students mostly use scientific criteria to formulate hypotheses, use better control of variables strategies, can more clearly describe the process and the phenomena involved, and decide the criteria for their hypotheses verification more successfully.