Granulocytopenia is thought to be the sole mechanism underlying the increased susceptibility to bacterial infection in hosts with anticancer chemotherapy. Little is known about the functional state of tissue macrophage populations in such hosts. Using a model of chemotherapy-induced leukopenia, the number and function of alveolar macrophages (AMS) were examined during and after multiple injections of an anticancer agent, cyclophosphamide (CP). Although CP quickly reduced peripheral blood leukocytes, the number of these cells rebounded quickly 3 to 4 days after the withdrawal of CP. Accompanying blood leukopenia was a profound reduction in the number of ams. Contrary to the rapid onset of blood leukopenia, tissue macrophage deficiency was a more chronic process that worsened gradually as the CP regimen continued. Of importance, in contrast to blood leukopenia, which restored itself shortly after CP withdrawal, tissue macrophage deficiency was not immediately self-recoverable in spite of a restored number of circulating leukocytes. Although AMS had a decreased ability to proliferate during, but not after, the CP regimen, these cells retained a normal ability to release tumor necrosis factor-α and nitric oxide. To identify the potential therapeutics for recovering macrophages, a gene vector expressing granulocyte macrophage–colony-stimulating factor (GM-CSF) was delivered either systemically or locally. GM-CSF transgene was able to expand macrophage populations only when delivered to the lung after, but not during, the CP regimen. This study thus identifies tissue macrophage deficiency as a mechanism of weakened innate immunity by chemotherapy and suggests the usefulness of topical GM-CSF transgene expression for restoring innate immunity in the lung.