The first two years of the iPhD program consists of coursework and writing a Master’s thesis. Here is the minimal credit requirement for each semester.
| Semester I | Semester II | Semester III | Semester IV | Masters Project | Total |
| 19 to 22 | 19 to 22 | 12 to 16 | 12 to 16 | 14 | 84 |
Integrated PhD students must register with a faculty by the end of their first year for their Master's project. IPhD students are expected to register for a combination basic/midlevel courses in their first year and graduate level courses in their second year. Here are the possibilities. Additionally, iphd students can also take topics courses running in any given semester (they are not listed below). In addition to these courses they can also take one reading course (3 credit) each semester.
| Fall Courses | Spring Courses | |
| Algebra | Galois Theory | Commutative Algebra Algebraic Number Theory |
| Graduate Algebra I | Graduate Algebra II | |
| Analysis | Measure Theory and Integration |
Functional Analysis Complex Analysis |
| Graduate Analysis I | Graduate Analysis II | |
| Geometry/Topology | Algebraic Topology | Calculus on Manifolds Differential Geometry |
| Graduate Topology I | Graduate Topology II | |
| Discrete Mathematics | Algorithms | Graph theory Cryptography or Coding theory |
| Differential Equations/Applicable Mathematics | ODE Probability |
Stochastic Processes PDE |