Objective To explore the application of two methods of direct fecal detection ofClostridium difficilein patients with recurrent inflammatory bowel disease (IBD), including nucleic acid amplification test (NAAT) and enzyme immunoassay (EIA), in order to provide support for hospitals to prevent and control clostridium difficile infection (CDI). Methods Fresh feces of 48 patients with recurrent IBD treated between November 2014 and April 2015 were collected within 48 hours after admission. Anaerobic culture and identification, NAAT and EIA were used to test the same samples. Statistical analysis was performed using Kappa test. Results Among the 48 fecal samples,Clostridium difficilewas negative in 37 and positive in 11 including 2 (4.2%) with toxigenicClostridium difficile characterized as toxin type A+B+. Compared with anaerobic culture and identification, NAAT had a perfect correlation (Kappa=1.00,P<0.05), and EIA had an almost perfect correlation (Kappa=0.89,P<0.05). But EIA toxin test had missed detection of toxigenic samples. Conclusions For patients with recurrent IBD combined with CDI, both NAAT and EIA test may be applied to detctClostridium difficile in feces directly, while NAAT may show a better performance. Samples from highly suspected patients with negative toxin result tested by EIA should be confirmed by other methods such as NAAT.