In the past 15 years, the incidence of Clostridium difficile infection has emerged especially because of the new highly virulent strains. The classical diagnosis methods used to diagnose C. difficile infection take time and the enzyme immunoassay (EIA) test has demonstrated the lack of sensitivity. Even though new modern molecular methods have become available, the diagnosis of C. difficile in patients or healthy carriers remains a big challenge for both clinicians and laboratory staff. In the present chapter, we will list the main genotyping methods, stressing their advantages and disadvantages, as well. A brief presentation of the most useful kit (principle, sensitivity, specificity, benefits and disadvantages) to assess the impact of molecular methods in comparison with classical methods will offer support for future research in the present context of an increasing prevalence of C. difficile infection that represents worldwide, a real public health problem. To improve the patients' quality of life, to limit hospital transmission, and to save money, we have tried to identify the best diagnosis algorithm as tool in C. difficile diagnosis and surveillance. This algorithm may differ depending on the capacities of the laboratories and on the socioeconomic level of the countries in question.