Bangladesh faced two epidemic waves of highly pathogenic avian influenza (HPAI) H5N1 in two consecutive years. The peaks of the waves were observed in February–July 2007 and January–April 2008, respectively. We examined the spatial and temporal patterns of the 293 outbreaks in 143 subdistricts in 2007 and 2008. Global clustering assessed by K-function was seen at distances 150–300 km between subdistricts. Significant local clusters were detected by space–time scan statistics. In both waves, significant primary clusters of HPAI outbreaks were identified in the central part of the country dominated by commercial production systems and in the northwestern part primarily in backyard production systems. Secondary clusters varied from the northwestern part in 2007 and the southern part in 2008. The findings are highly relevant for the successful planning and implementation of control, prevention and surveillance strategies by highlighting areas where detailed investigations should be initiated.