In this paper, we derive a boundary-domain integral formulation for the vorticity transport equation under the assumption that the viscosity of the fluid, through which the vorticity is transported by diffusion and convection, is spatially changing. The vorticity transport equation is a second order partial differential equation of a diffusion-convection type. The final boundary-domain integral representation of the vorticity transport equation is discretized using a domain decomposition approach, where a system of linear equations is setup for each sub-domain, while subdomains are joint by compatibility conditions. The validity of the method is checked using several analytical examples. Convergence properties are studied yielding that the proposed discretization technique is second order accurate for constant and variable viscosity cases.