Mathematics and Science Teaching Corps Act of 2006

Mathematics and Science Teaching Corps Act of 2006 - Amends the Department of Education Organization Act to create a Math and Science Teaching Corps to significantly improve mathematics and science achievement among secondary school students.

Requires the Director of the Corps to carry out a program that awards: (1) Math and Science Teaching Corps Fellowships for Prospective Teachers (MSTC Fellowships) to teachers possessing comprehensive subject area knowledge; (2) grants to partner institutions to pay the tuition, fees, and overhead costs of the fellows; and (3) grants to participating local educational agencies to pay the expenses associated with facilitating the induction and professional development services for the fellows.

Requires MSTC Fellowship recipients to: (1) receive specified pedagogical training; (2) teach mathematics or science, for a specified stipend, in a public secondary school for four years, and participate in induction and professional development programs; (3) participate in additional weekend or summer professional development activities in their first two years of teaching; and (4) receive mentoring training in their third year of teaching, and provide mentoring in their fourth year.

Requires the Director to carry out a program that awards Math and Science Teaching Corps Fellowships for Experienced Teachers (MSTC Master Fellowships). Requires an MSTC Master Fellowship recipient to: (1) continue to teach mathematics or science, for a specified stipend, in a secondary school of a participating agency for at least five of the seven years after receiving such fellowship; (2) serve as a leader and mentor within the individual's department and school; and (3) attend subject or pedagogy workshops offered by the participating local educational agency.

Requires that at least 30% of the recipients in each category of fellowship teach at hard-to-staff schools. Provides bonus stipends to such recipients.