The airborne dissemination of Clostridium difficile (C. difficile) endospores (spores) in healthcare environments is documented in multiple studies. Once airborne, spores have the potential for transport on air currents to other areas. This study compared the methods in the collection of C. difficile spore aerosol. This study determined the relative efficiency of commonly used bioaerosol air sampling methods when characterizing airborne C. difficile spore concentrations. Air samplers evaluated in this study were the AirTrace slit-to-agar impactor, AGI-30 impinger, SKC BioSampler impinger, and a 47-mm mixed cellulose ester (MCE) filter cassette. Non-toxigenic C. difficile spores were nebulized into an enclosure contained in a biological safety cabinet. Side-by-side air samples were drawn from the enclosure. The slit-to-agar impactor, successfully used in previous studies to collect airborne spores, served as the reference method. Relative efficiency for the 47-mm MCE filter cartridge was higher than the slit-to-agar impactor (mean 136.6%, 95% CI 124.7–148.5%). Efficiencies of the impingers were similar and were low (mean 4.13%, 95% CI 2.27–5.99%). Impingers failed to maintain culturability of C. difficile spores during sampling. This study is the first to compare the efficiencies of commonly used bioaerosol sampling methods to collect airborne C. difficile spores. Filter air sampling provided the greatest collection of airborne spores. Slit-to-agar air sampling may underestimate the number of airborne spores present. Impinger air sampling could significantly underestimate the actual number of airborne C. difficile spores present or fail to detect airborne spores.