The main objective of this four-year empirical research project has been to develop the experimental design skills of 12-16 year-old Hungarian pupils in Grades 7-10 of junior high school through guided inquiry, using six chemistry experiment worksheets each school year. Group 1 (control group) and Group 2 follow step-by-step instructions, but after the experiment, Group 2 also answers a series of questions about the design of the experiment. Group 3 is required to design the experiments, guided by the series of questions. The impact of the intervention on 603 pupils' experimental design skills and disciplinary content knowledge were measured by structured tests at the beginning of the project and at the end of three school years. By the end of the third year the intervention only had a small positive effect on the development of experimental design skills in Group 3 (Cohen's d: 0.16), while the development of disciplinary content knowledge was slightly negatively affected for both experimental groups (Cohen's d for group 2: -0.07; Cohen's d for group 3: -0.19).