Background: Although teaching nature of science (NOS) has been continually emphasized in many major reform efforts in science education, researchers claim that students do not possess adequate views of NOS. Insufficient understanding of NOS can be associated with the ineffectiveness of curricular or instructional approaches. Consequently, researchers have begun to examine ways to improve students' understanding of NOS. In this study, we purposely focused on honored students who major in the sciences to see whether extended science programs develop better understanding of NOS. We aimed to understand the relationship between science instruction and students' NOS understanding in Israeli science advanced placement courses. Semi-structured interviews with science teachers provided data about the instruction of science in general, and NOS instruction in particular. An open-ended questionnaire that dealt with global climate change assessed students' understanding of NOS. Results: Teachers reported about limited and implicit instruction about NOS. Although teachers believed that teaching NOS is important, the need for their students to succeed in the high-stake matriculation exams and the fact that these exams do not include questions dealing with NOS were indicated as the main reasons for the teachers' reluctance to teach NOS. Nevertheless, we found a small overall improvement in students' understanding of NOS. Two possible factors probably contributed to students' improved understanding of NOS: conducting inquiry projects and teaching cases in history of science. Yet, in both contexts, the understanding improved only in one aspect of NOS. Conclusions: The small improvement in understanding NOS reflects the limited and non-systematic teaching of NOS. Implicit instruction is not effective enough to promote understanding of NOS, even in advanced 2-year science program, where both students and teachers are highly capable. Other factors that could explain the little improvement are insufficient subjects in the curriculum that emphasize NOS and teaching methods that do not encourage discussion about NOS.