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The effect of hydroxypropyl-α-cyclodextrin (HP-α-CD) complexation on in vitro pulmonary deposition of a cyclic peptide cyclosporin A (CsA) was studied. In addition, the effect of storage (32 days, 40 °C, 75% RH) on CsA/HP-α-CD complexes was studied. The complexation of CsA with CDs was evaluated by a phase-solubility method. Solid CsA/HP-α-CD complexes were prepared by freeze drying. Three inhalation formulations were prepared: CsA/lactose reference formulation (LF) (drug:carrier 1:364, w/w), CsA/HP-α-CD complex formulation (CDF) (drug:CD 1:269, w/w) and CsA/HP-α-CD complex/lactose formulation (CDLF) (complex:carrier 100:114, w/w). The inhalation studies were performed in vitro using Andersen Sampler (Ph. Eur.) and Taifun® multi-dose dry powder inhalers (DPIs). Before the storage, the respirable fraction value (RF%) of CsA was 19.8 ± 0.7%, 33.0 ± 7.0% and 34.6 ± 1.1% (mean ± S.D., n = 4 × 20) with LF, CDF and CDLF, respectively. When exposed to moisture (storage in a permeable polystyrene tube), the RF% values of CsA from formulations containing CsA/HP-α-CD complexes were lower than before the storage. However, when stored in the Taifun® DPI, the RF% value of CsA from any of the formulations did not decrease. In conclusion, an acceptable RF% value of a peptide CsA from freeze-dried, simply micronized CsA/HP-α-CD complex powder was achieved before and after storage in the DPI.