The space-time scan statistic is often used to identify incident disease clusters. We introduce a method to adjust for naturally occurring temporal trends or geographical patterns in illness. The space-time scan statistic was applied to reports of lower respiratory complaints in a large group practice. We compared its performance with unadjusted populations from: (1) the census, (2) group-practice membership counts, and on adjustments incorporating (3) day of week, month, and holidays; and (4) additionally, local history of illness. Using a nominal false detection rate of 5%, incident clusters during 1 year were identified on 26, 22, 4 and 2% of days for the four populations respectively. We show that it is important to account for naturally occurring temporal and geographic trends when using the space-time scan statistic for surveillance. The large number of days with clusters renders the census and membership approaches impractical for public health surveillance. The proposed adjustment allows practical surveillance.