This article reports on an analysis of alignment between NY state core curricula and NY Regents tests in physics and chemistry. Both the curriculum and test were represented by a two dimensional table consisting of topics and cognitive demands. The cell values of the table were numbers of major understandings in the curriculum and points of test items in the test. The Porter alignment index was computed for each test. It was found that, overall, there was a high alignment between the NY core curriculum and the NY Regents test, and the alignment remained fairly stable from test to test. However, there were considerable discrepancies in emphases on different cognitive levels and topics between the core curriculum and the test. Issues related to the nature of alignment, and the nature and validity of content standards were raised, and implications for science curriculum and instructions were also discussed.