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This study is intended to develop the experimental module for the transpiration, and to apply it to the high school biology classes and determine the effectiveness of improving scientific thinking, science inquiry skills and affective domains related to science. The module is composed of a worksheet for students and a teachers' guide and lets learners for themselves make a hypothesis, design an experiment and answer questions raised by learners. The subject of this study was four classes of 11th graders majoring in the realm of nature and attending "H" high school located in Gumi City. Of these, two classes are the experimental group and the others are the control. Each three class hours of instructions were provided for them. The experimental group was taught by the module, while the control group was taught by the traditional way of doing experiments. The results are as follows: The experimental group had more meaningful effectiveness in scientific thinking ability, inquiry skills and affective domains related to science such as interest and attitude than the control group. Interestingly, scientific thinking has more to do with science inquiry skills in terms of a correlation coefficient(0.579). It means that the students with higher scientific thinking ability tend to have higher science inquiry skills. Consequently, this study revealed that the experimental module developed in this study was more effective than the traditional way of doing experiments in the areas of scientific thinking, science inquiry skills, and interest and attitude of affective domains related to science. The results suggested that more experimental modules considering students' process skills are necessary to develop and introduce to the biology classes for the secondary school students.