Implicit in all US science education reform efforts in the past, is equal access and opportunity to learn science for all students regardless of their background and status. However, most science teacher preparation programs (with some exceptions, i.e., those that offer dual endorsement/certification), do not have the capacity or resources to prepare teachers to serve special education students. The paper examines the relationship between urban secondary science teachers and special education students. It interrogates the notion of "Highly Qualified Teacher" (HQT), by comparing a sample of science teacher preparation programs in the Greater New York City area, the standards for science teacher preparation and the needs and requirements for serving students with special needs in the science classroom. Using teacher preparation program data published on institutional websites, cross-referenced with data published on the New York State Education Department website, the paper reviews thirteen secondary science teacher preparation programs based on four criteria relating to science content and pedagogical content knowledge, special education courses/practicum offered, multicultural pedagogy and preparation in action research and reflection. The paper demonstrates that despite best efforts, there is a misalignment between the preparation of urban science teachers and the needs and requirements of the special education students they serve. To meet the needs of all learners in the science classroom, including special education students, the paper proposes that urban science teachers must demonstrate knowledge and competencies in planning, implementing and evaluating project-based science instruction. A framework for accomplishing this is discussed, including assumptions, limitations and policy implications.