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This study was to develop instructional programs for elementary school students in which we reflected their preconceptions and typical emotions on bacteria and to apply them. They were developed using 5E learning cycle instructional model to change misconceptions and negative emotion regarding bacteria into biologically acceptable conceptions and positive emotion on them. They consist of two kinds of versions: teachers' guide and students' worksheet. To develop more practical programs, they had gotten a pilot study with 24 upper graders of elementary school students and been ameliorated three times. Seven classes titled as ‘life as a bacteria, ’the size of bacteria', ‘the shape of bacteria', ’bacteria-infested place', ‘the usefulness of bacteria' and ’the importance of bacteria in human life' were conducted and applied to 33 fourth graders during one semester. The effectiveness of the program were tested by specially designed three kinds of instruments: test on the conception of bacteria, the emotion on bacteria and interview guide. These were administrated three times such as before, after and far after and analyzed quantitatively and qualitatively. In first result, most of the subjects have non-scientific conceptions and negative emotion about bacteria. Because Korean science curriculum has barely included about microorganism, elementary school students' personal experience such as visiting dental office, the hospital or TV programs including animation for bacteria characters could be affected their preconception and emotions on it. Secondly, the classes using special programs on bacteria had significantly effectively worked to change preconception of misconceptions and negative emotion on bacteria into scientific conceptions and positive prospect on it. The effectiveness of the programs make school science curriculum have to include biological contents regarding microorganism.