Self-Assembled Monolayers (SAMs) are used in areas as diverse as corrosion protection; nanodevices and biotechnology. Despite a wealth of both experimental and theoretical studies of SAM structure and behaviour[1]; there still remain some unanswered questions. Alkanethiol molecular ink diffusion on alkanethiol SAMs is one such area; and one amenable to computational study. Ink diffusion is an important consideration when one performs microcontact printing - "... the quality of the printed pattern strongly depends on the mobility of the ink compound ..."[2]. An understanding of ink diffusion is therefore crucial to the production of stable; high-resolution nanopatterns. We first of all calculated alkanethiol self-diffusion coefficients in bulk liquid and obtained good agreement with measured values. The Einstein diffusion equation was used to calculate the diffusion coefficients from 1 nanosecond molecular dynamics (MD) simulations Simulations of alkanethiol SAMs were performed and the temperature dependence of the SAM tilt angle found to be in good agreement with literature values. Having validated our method both for calculating diffusion and the SAM structural models; we calculated the diffusion of both a single alkanethiol molecule and a 75-molecule drop ; on a range of perfect and defect SAMs; establishing a range for ink diffusion in different environments and; ultimately; allowing identification of optimum ink molecular weights for microcontact printing applications