In small airways, Clara cells are the main epithelial cell type and play an important physiological role in surfactant production, protection against environmental agents, regulation of inflammatory and immune responses in the respiratory system. Thus, Clara cells are involved in lung homeostasis and pathologies like asthma, Chronic Obstructive Pulmonary Diseases (COPD) or cancers. To date, Clara cells implication in these pathological processes remains largely enigmatic. The engineering of a transgenic strain mouse allowing specific gene invalidation in Clara cells may be of interest to improve our knowledge about the genes involved in these diseases. By using the Cre/loxP strategy we report the engineering of a transgenic mouse strain with expression of Cre recombinase under the control of the Clara Cell Secretory Protein (CCSP) promoter. Specific staining and immuno-histochemistry performed after breeding with reporter mice revealed that CCSP drives a functional Cre expression specifically in Clara cells. This mouse strain is a powerful tool for Cre-loxP-mediated conditional recombination in the lung and represents a new tool to study Clara cell physiology.