This article addresses an important aspect of the analysis of metapopulation persistence. It highlights some consequences of ignoring and including stochasticity in the sequence of extinction and colonization events. The results are based on a comparative analysis of the outcomes of two (one deterministic, one stochastic) spatially realistic metapopulation models and a search for common effects and differences. One key result of the article is that, under certain conditions, there are extra effects of the landscape structure (number and configuration of patches, patch size distribution) on metapopulation persistence if stochasticity is included. In these cases, ignoring or including stochasticity can change conclusions about the persistence status but also ranking orders, relative results, and qualitative trends. A list of conditions is provided under which including stochasticity is vital to prevent counterproductive conclusions about metapopulation persistence. The results of the overall study are condensed in five lessons about the effect of stochasticity. A number of implications for ecological theory and conservation management are discussed. The study demonstrates the potential of three recently published approximation formulas (metapopulation capacity (lambda)M, mean lifetime Tm, and effective number of patches ) to serve as tools for ecological analysis and thinking.