Automated image analysis of bronchial tissue offers the opportunity to quantify stained area and staining intensity in a standardized way to obtain robust estimates of inflammatory cell counts and cytokine expression from multiple large areas of histopathologic sections. We compared fully automated digital image analysis with interactive digital cell counting and semiquantitative scoring of cytokine expression in terms of repeatability and agreement in bronchial biopsies in 52 patients with mild to moderate atopic asthma. Immunohistochemistry with antibodies against CD3, interleukin (IL)-4, IL-5, and interferon-gamma protein was performed on frozen tissue sections, using 3-amino-9-ethylcarbazole as chromogen and hematoxylin as counterstaining. IL-4 and IL-5 messenger RNAs were localized by in situ hybridization without hematoxylin staining. Separation of 3-amino-9-ethylcarbazole and hematoxylin-stained pixels was achieved by linear combination of red- and blue-filtered gray-scale images. Using baseline biopsy specimens, fully automated CD3+ cell counts showed perfect repeatability (r = 1.0) and a strong linear relationship with the interactive procedure (r = 0.98). Automated densitometry showed perfect repeatability (1.0) and a moderate to strong relationship with semiquantitative scoring of protein and messenger RNA expression (r = 0.43-0.89). Relationships between automated and semiquantitative assessments of changes in cytokine expression during 2 years of follow-up were moderate to strong (r = 0.40-0.84). We conclude that fully automated cell counts and automated densitometric analyses in bronchial tissue of patients with asthma are unbiased and help to reduce variability in inflammatory outcomes.