A study was undertaken to examine the isolation rate of Klebsiella pneumoniae from birds affected by natural outbreaks of highly pathogenic avian influenza (H5N1) that occurred in Nigeria between December, 2006 and July, 2007. A total of 100 birds from 114 commercial, backyard and free range flocks infected with H5N1 virus within the study period were sampled. A total of 600 tissues (heart, lung, spleen, liver, trachea and intestine), 100 each from the 100 birds were collected for bacteriology. Data generated was entered into Microsoft excel, while descriptive statistical analysis was conducted using SPSS (Version 12.01). Klebsiella pneumoniae was isolated from 9 (1.5%) samples. The organism was isolated from the liver, lungs and trachea of commercial layers and turkeys. During the HPAI outbreaks, Klebsiella pneumoniae was isolated from 9 different flocks with a total of 21,805 birds, mortality rate of (7.3%) and proportionate mortality rate of (2.5%). The bacterium was not isolated from H5N1 free flocks which served as control. The result of this study indicated that Klebsiella pneumoniae may have acted as a secondary pathogen to aggravate the clinical signs during H5N1 outbreaks that occurred in Nigeria.