We investigated the alternative conceptions of secondary school students on respiration. The pencil-test (the explanation-after-selection type test) was chosen as the investigating method, By using systematic network analysis; the test responses were analyzed from secondary schools in Seoul. As a result, the ratio of alternative conceptions had a different range at each item. In definition of respiration many students (35.1%) thought respitation as gas exchange and 53% of them mentioned energy. Many students considered photosynthesis as day light-respiration in plant and respiration site as gas exchange site such as leaves in plant and lung in animal. Many students mentioned parasites and single cell organisims had na respiration. Many of the 8th grade students thought energy was not obtained from respiration, but from digestion or absorption. A few students mentioned yeasts produced oxygen in anaerobic respiration. This result may be helpful to the design of biology instructions in secondary school.