The lung is continuously exposed to the environment, therefore it is a prime target for infectious diseases. Especially chronic lung diseases infections contribute significantly to morbidity and mortality. Cystic fibrosis (CF) is a genetic disorder with a prominent pulmonary phenotype. Patients suffer from mucus plugging and chronic lung infections resulting in bronchiectasis. Pulmonary function declines over the first decades in life and often, in end-stage lung disease, lung transplantation becomes the only viable therapeutic option. We are interested in characterisation of the interaction of immune cells in pulmonary inflammatory disease and in developing novel techniques for the detection and classification of pathogens in fixed and embedded tissue. The figure shows bacteria detected on nasopharyngeal mucosa with specific rRNA in situ hybridisation and classic necrotizing granulomas – the hallmark of (specific) infections with mycobacteria.