This article examines secondary students' design of experiments after engagement in an innovative and inquiry-oriented module on heat transfer. The module consists of an integration of hands-on experiments, simulated experiments and microscopic model simulations, includes a structured series of guided investigative tasks and was implemented for a sample of 24 lower secondary (compulsory education) school students in Greece. A post-instructional assessment comprising written tests and interviews of the sample of students was employed. The findings revealed that after implementation of the module, a respectable number of the students showed ability in experiment design skills such as forming hypotheses and successfully describing experimental procedure. (Contains 1 figure.)