Matriculation 2000 was a 5-year project aimed at moving from the nationwide traditional examination system in Israel to a school-based alternative embedded assessment. Encompassing 22 high schools from various communities in the country, the Project aimed at fostering deep understanding, higher-order thinking skills, and students' engagement in learning through alternative teaching and embedded assessment methods. This article describes research conducted during the fifth year of the Project at 2 experimental and 2 control schools. The research objective was to investigate students' learning outcomes in chemistry and biology in the Matriculation 2000 Project. The assumption was that alternative embedded assessment has some effect on students' performance. The experimental students scored significantly higher than their control group peers on low-level assignments and more so on assignments that required higher-order thinking skills. The findings indicate that given adequate support and teachers' consent and collaboration, schools can transfer from nationwide or statewide standardized testing to school-based alter-native embedded assessment. © 2003 Wiley Periodicals, Inc. J Res Sci Teach 40: 34–52, 2003