The purpose of the study was to evaluate if the level and aspects of critical thinking of the pupils are influenced by peer interaction promoted in science classrooms, or by the science activities implemented or yet, by both factors. A factorial design 2x2 was carried out. During one academic year. Four different treatments were implemented randomly. The sample size was 144 pupils of the 5th and 6th grades. They were from three different Portuguese schools located in Portalegre city or nearby. The results point out that peer interaction as a learning strategy enhances critical thinking skills. Some implications of the study can be drawn for science education, teacher education and educational research.