Over 3 years (1999-2002), 305 cases of falciparum malaria were diagnosed in Toulouse, France. After retrospective analysis, only 131 patients entered the study. The diagnosis of malaria was ensured by optical methods (QBC then thin smear examination), the results of which were checked from 1999 to mid-2001 by a conventional PCR method, replaced at that time by a real-time PCR using LightCycler. To detect Pfcrt K(lysine)76T(threonine) mutation, a real-time PCR assay was developed, the sensitivity of which was one mutated parasite per microliter, or 2% mutant asexual forms in a mixed population. Eighty-one patients harbored only mutant parasites, and 11 had a K76K/T76-mixed infection. The distribution of K76T mutation was significantly affected by the use of a chloroquine + proguanil (CQ + P) prophylaxis (P = 0.00037). Among 96 subjects who had no exposure to chloroquine or any history of CQ + P prophylaxis, the mean parasitemia was higher in K76-infected patients (P = 0.038), which suggested a lack of virulence in the falciparum mutant population.