The cells of the innate immunity (epithelial alveolar cells and macrophages) normally clear the inhaled Aspergillus conidia. These cells produce mediators that are able to recruit neutrophils and activate cellular immunity in order to kill the potentially invasive fungus forms (hyphae). The suppression of these mechanisms, including the suppression of the T cell responses, plays a determinant role in the occurrence of the disease and the type of the disease. Infection can disseminate to other organs.

Aspergillosis most frequently affects the lungs since the respiratory tract is the main portal of entry. Typical forms are:

1. Invasive pulmonary aspergillosis (IPA): this entity is typically associated with use of immunosuppressive therapies, corticosteroids, or coinfections in immunocompromised patients (especially hematological malignancies). It is characterized by invasion of pulmonary vasculature by the Aspergillus hyphae with subsequent lung damage.
2. Chronic cavitary pulmonary aspergillosis (CCPA): this entity is typically found in non immunocompromised patients with prior or current lung disease (such as tuberculosis). It is defined as one or more pulmonary cavities with serological or microbiological evidence of Aspergillus spp and a history of at least 3 months of chronic pulmonary symptoms or progressive radiologic abnormalities.
3. Aspergilloma: this entity is typically found in nonimmunocompromised patients with prior or current lung disease (such as tuberculosis). It is defined as a single pulmonary cavity containing a fungus ball with microbiological or serological evidence of Aspergillus spp and a history of minimal or no symptoms and no radiographic progression over a 3 months of observation.
4. Allergic bronchopulmonary aspergillosis (ABPA): this entity is typically found in patients with asthma and cystic fibrosis. There are recurrent asthma exacerbations caused by a hypersensitivity reaction to the fungus. It is associated with elevated Aspergillus-specific IgE, elevated total IgE, detectable Aspergillus-specific IgG, eosinophilia and positive skin prick tests for Aspergillus.

Aspergillus spp can disseminate beyond the respiratory tract to multiple different organs, including the brain. Typical patterns observed in brain imaging are cerebral abscesses or cortical and subcortical infarction. The prognosis is poor.