The purpose of this qualitative interpretive research study was to examine high school students' written scientific explanations during biology laboratory investigations. Specifically, we characterized the types of epistemologies and forms of reasoning involved in students' scientific explanations and students' perceptions of scientific explanations. Sixteen students from a rural high school in the Southeastern United States were the participants of this research study. The data consisted of students' laboratory reports and individual interviews. The results indicated that students' explanations were primarily based on first-hand knowledge gained in the science laboratories and mostly representing procedural recounts. Most students did not give explanations based on a theory or a principle and did not use deductive reasoning in their explanations. The students had difficulties explaining phenomena that involved intricate cause-effect relationships. Students perceived scientific explanation as the final step of a scientific inquiry and as an account of what happened in the inquiry process, and held a constructivist-empiricist view of scientific explanations. Our results imply the need for more explicit guidance to help students construct better scientific explanations and explicit teaching of the explanatory genre with particular focus on theoretical and causal explanations.