Ground shaking intensity varies spatially in earthquakes, and many studies have estimated correlations of intensity from past earthquake data. This paper presents a framework for quantifying uncertainty in the estimation of correlations and true variability in correlations from earthquake to earthquake. A procedure for evaluating estimation uncertainty is proposed and used to evaluate several methods that have been used in past studies to estimate correlations. The results indicate that a weighted least squares algorithm is most effective in estimating spatial correlation models and that earthquakes with at least 100 recordings are needed to produce informative earthquake‐specific estimates of spatial correlations. The proposed procedure is also used to distinguish between estimation uncertainty and the true variability in model parameters that exist in a given data set. The estimation uncertainty is seen to vary between well‐recorded and poorly recorded earthquakes, whereas the true variability is more stable.