The present understanding of the pathophysiology of community-acquired pneumonia (CAP) explains the mechanism for many specific manifestations, but does not address adequately why only some patients experience complications. Recent advances in under-standing the genetics of complex illnesses offer hope for a more complete insight into the pathogenesis of CAP. This article reviews genetic variation in the molecules involved in the known patho-genic mechanisms of CAP, including cough, bacterial recognition, inflammation and the compensatory anti-inflammatory response,and organ dysfunction.