Effects of the class size and teaching methods on academic achievement of Japanese pupils of thirty four elementary schools at three cities are analyzed by using generalized linear model, structural equation models and multilevel models. It was found that class size, team-teaching and small group teaching had no or very small effects on pupil's achievement. But, some teaching methods, such as reading book activity in the morning before formal lesson, and not-one-way teaching found to have a significant effect on achievements. It was also found that order in the classroom had positive significant effect on average achievement of the schools.