Multicomponent lipid membranes in the liquid phase exhibit dynamic lateral heterogeneities which play an important role in specific cell membrane functions. A GPU-based parallel algorithm for two-dimensional lattice Dynamic Monte Carlo simulations of nanodomain formation in binary lipid membranes was developed and tested. Speedups of up to 50-times over CPU-based calculations were achieved, and simulations employing lattices of up to 1800 × 1800 sites were performed. The existence of large nonregular lipid domains of sizes up to 160 nm was demonstrated. This reveals the necessity to employ lattices of at least ∼900 × 900 sites to study the lateral lipid organization in complex lipid membranes.