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The spatial scan statistic method has been widely used for detecting disease clusters. Its results may be affected by scales, including the aggregation level of the input data and the population threshold used in the detection. Previous studies offered inconsistent findings, and few had considered both types of scales at the same time. Using 24 simulated datasets and two real disease datasets, we investigated the method's sensitivity to the two types of scales. We aggregated the individual-level data into areal units of three levels, including county, town, and a 900 m grid. We detected clusters with three population thresholds, including 10%, 25%, and 50%. We used two measurements, distance between cluster centres and the Jaccard index, to quantify the consistency of clusters detected with different scale settings. We find: (1) the method is not greatly sensitive to the data aggregation level when the cluster is strong and in a place with high population density; (2) the method's sensitivity to the population threshold is determined by the actual size of the true cluster; and (3) a regular grid with fine resolution is advantageous over the subjectively defined areal units. The process and findings may have broader meanings to similar spatial analyses. [ABSTRACT FROM AUTHOR]