The emergence of the anterior-posterior body axis during early gastrulation constitutes a symmetry-breaking event, which is key to the development of bilateral organisms, and its mechanism remains poorly understood. Two-dimensional gastruloids constitute a simple and robust framework to study early developmental events in vitro. Although spontaneous symmetry breaking has been observed in three dimensional (3D) gastruloids, the mechanisms behind this phenomenon are poorly understood. We thus set out to explore whether a controllable 2D system could be used to reveal the mechanisms behind the emergence of asymmetry in patterned cellular structures. We first computationally simulated the emergence of organization in micro-patterned mouse pluripotent stem cell (mPSC) colonies using a Turing-like activator-repressor model with activator-concentration-dependent flux boundary condition at the colony edge. This approach allows the self-organization of the boundary conditions, which results in a larger variety of patterns than previously observed. We found that this model recapitulated previous results of centro-symmetric patterns in large colonies, and also that in simulated small colony sizes, patterns with spontaneous asymmetries emerged. Model analysis revealed reciprocal effects between diffusion and size of the colony, with model-predicted asymmetries in small pattern sizes being dominated by diffusion, and centro-symmetric patterns being size-dominated. To test these predictions, we performed experiments on micro-patterned mPSC colonies of different sizes stimulated with Bone Morphogenetic Protein 4 (BMP4), and used Brachyury (BRA)-GFP expressing cells as pattern readout. We found that while large colonies showed centro-symmetric BRA patterns, the probability of colony polarization increased with decreasing sizes, with a maximum polarization frequency of 35% at ∼200μm. These results indicate that a simple molecular activator-repressor system can provide cells with collective features capable of initiating a body-axes plan, and constitute a theoretical foundation for the engineering of asymmetry in developmental systems.