We investigated the perception and preferred type of question and analyzed type of questions asked by teachers in elementary science class to identify how teachers' perception of questioning is reflected in teaching practices. We collected the data from questionnaires, deep-interview and audiotaped four classes from grade 3 and six classes from grade 6. The data form deep-interview were analyzed interpretively and Blosser' framework of question was used to analyze questions which teachers used in classes. By interpretation of data from questionnaires, the teachers agreed that questioning affects science class in elementary school. There were a little differences in perceptions of questioning among three teachers. They preferred various types of question rather than a specific type. They didn't have a good understanding of questioning. The result showed that the teachers used frequently cognitive-memory question and convergent thinking question, which belonged to closed questions in their science classes. This didn't accord with their preferred types of question. The causes came from objectives of science instruction, degree of understanding about questioning, preference and confidence for science class. From this findings, we suggested that teachers should be given opportunities to take training courses in questioning in order to use effective questioning in science class.