Asking learners standardized questions during performance of a self-directed inductive learning task might be a useful way to complement think aloud protocol data. However, asking questions might also scaffold the learning process and thus influence the exact processes one wants to study. In the study described in this paper two groups of learners performed a computerized self-directed inductive learning task in which they conducted experiments to discover the relations between five independent variables and one dependent variable. In one condition, the learners thought aloud, in the other the learners were asked additional standardized questions pertaining to specific reasoning steps during learning. Measures of learning outcome and learning processes were collected. It appeared that the questions did not influence learning outcome. With respect to learning processes no differences were found, except that learners in the no questioning condition more often repeated experiments. It was concluded that the questions do not seem to threaten the validity of research findings. © Taylor & Francis Ltd.