Optimal post-transplantation immunosuppression is critical to the survival of the graft and the patient after lung transplantation. Immunosuppressant agents target various aspects of the immune system to maximize graft tolerance while minimizing medication toxicities and side effects. The vast majority of patients receive maintenance immunosuppressive therapy consisting of a triple-drug regimen including a calcineurin inhibitor, a cell cycle inhibitor and a corticosteroid. Although these immunosuppressant drugs are frequently used after transplantation and to control inflammatory processes, limited data are available with regard to their effects on cells other than those from the immunological system. Notably, the airway epithelial cell is of interest because it may contribute to development of bronchiolitis obliterans through production of pro-inflammatory cytokines. This review focuses the current armamentarium of immunosuppressant drugs used after lung transplantation and their main side effects upon airway epithelial cells and mucociliary clearance.