This paper presents a mathematical methodology for transit route network optimization. The goal is to provide an effective computational tool for the optimization of large-scale transit route networks. The objectives are to minimize transfers and optimize route directness while maximizing service coverage. The formulation of the methodology consists of three parts: (1) representation of transit route network solution space; (2) representation of transit route and network constraints; and (3) solution search schemes. The methodology has been implemented as a computer program and has been tested using previously published results. Results of these tests and results from the application of the methodology to a large-scale realistic network optimization problem in Miami-Dade County, Florida are presented.