The purpose of this study is to determine the patterns of differences between genders in science achievement. Eleventh grade, 140 female and male students were sampled from a school in Seoul. According to the analysis results of pilot study, 20 items were finally selected for the main study. To sharpen our interpretations of the factors and provide some confirmation, we supplemented the statistical analysis with a more detailed cognitive study of the items using think-aloud protocols and interviews with student test takers. The analysis of this study took into account the different item formats, contexts, and presentation styles. The findings are as follows: First, there was no significant gender difference between multiple-choice and open-ended items. Second, male students achieved significantly better in the context of everyday life in multiple-choice items. Third, male students favored items presented as written texts. Fourth, in problem-solving process, female students tend to apply their science concepts, whereas male students tend to apply their everyday experiences. The results of this investigation indicate that gender difference in science achievement depends heavily on item characteristics.