A longitudinal study has been conducted to explore the impact of a new language policy for Hong Kong secondary schools on science learning. According to this policy, only schools that recruit the best 25% of students can teach science in English, the students' second language, while the other schools have to teach science in Chinese, the students' native language. The study involved a student cohort of 100 schools starting from S1 for three years. The outcome of science learning is conceptualized as consisting of students' achievement and self-concept in science. This paper reports the possible effects of English-medium instruction (EMI) and Chinese-medium instruction (CMI) on students' self-concept in science, as measured by students' responses to a questionnaire. Comparing with the CMI students, the EMI students showed higher self-concepts in Chinese, English and Mathematics, but a lower self-concept in science. This finding suggests that the EMI students might experience greater learning problems in science than in other subjects, probably because science learning involves abstract thinking and the mastery of scientific terminology which make a high demand on language proficiency. The EMI students showed a greater interest in learning science than the CMI students, indicating that they were more academically oriented. The EMI students, however, formed a lower perceived self-competence in science than their CMI peers, despite that they performed better in the science achievement test than many of the CMI students. This perception supports the view that using English for instruction may have negative effects on science learning. It is also consistent with the observation that the EMI students perceived science as more difficult to understand and learn than the CMI students.