Symmetry breaking in a population of living cells occurs even under uniform conditions, leading to heterogeneity in the population. An example for such a process can be seen in the response of bacterial populations to antibiotics, termed ‘persistence’. The mechanism for persistence is unknown. We present a detailed study of the module implicated in antibiotic persistence. We find that noise, which is inherent in biological systems, results in the co-existence of dormant and growing cells. Stochastic simulations of protein-protein interactions offer predictions for the molecular mechanism behind high persistence, which have been confirmed by our measurements