Spore germination is an important part of the pathogenesis of Clostridium difficile infection (CDI). Spores are resistant to antibiotics, including those therapeutically administered for CDI and strains with a high germination rate are significantly more likely to be implicated in recurrent CDI. The role of germination efficiency in cases of refractory CDI where first-line therapy fails remains unclear. We investigated spore germination efficiencies of clinical C. difficile isolates by measuring drop in OD600 and colony forming efficiency. Ribotype 027 isolates exhibited significantly higher germination efficiencies in the presence of 0.1 % (w/v) sodium taurocholate (51.66±8.75 %; 95 % confidence interval (CI) 47.37–55.95 %) than ribotype 106 (41.91±8.35 %; 95 % CI 37.82–46 %) (P<0.05) and ribotype 078 (42.07±8.57 %, 95 % CI 37.22–46.92 %) (P<0.05). Spore outgrowth rates were comparable between the ribotype groups but the exponential phase occurred approximately 4 h later in the absence of sodium taurocholate. Spore germination efficiencies for isolates implicated in severe CDI were significantly higher (49.68±10.00 %, 95 % CI 47.06–52.30 %) than non-severe CDI (40.92±9.29 %, 95 % CI 37.48–44.36 %); P<0.01. Germination efficiencies were also significantly higher in recurrent CDI or when metronidazole therapy failed than when therapy was successful [(49.00±10.49 %, 95 % CI 46.25–51.75 %) versus (41.42±9.43 %, 95 % CI 37.93–44.91 %); P<0.01]. This study suggests an important link between C. difficile spore germination, CDI pathogenesis and response to treatment; however, further work is warranted before the complex interplay between germination dynamics and CDI outcome can be fully understood.