The purpose of this study is to develop a framework for analyzing classroom argumentation that includes a process of rebutting. A most commonly used framework to analyze argument in science education is Toulmin's Argumentation Pattern. It is useful for analyzing argumentation but it cannot represent the complexity of students' rebuttals during argumentations in the lessons. The study was conducted in three science stream classes of grade twelve students. The number of students in each class ranged from 39 to 40 students with a total of 119 students. The topics of the lessons were three biology contents that are closely related to socio-scientific issues, i.e., genetics, evolution, and biotechnology. Analyses of students' rebuttals show that the newly developed Rebuttal Analysis Framework generated a better picture of classroom argumentation. In terms of the level of students' argumentation, this study shows that argumentation-oriented lessons do not necessarily lead to the improvement of students' argumentation competence. The study also identifies four types of argumentation changes, namely inert, contrary, under two positions, and impartial.