Aims To investigate the distribution of cytochrome P450 2C9 ( CYP2C9 ) and 2C19 ( CYP2C19 ) genotype frequencies in the Beninese and Belgian Caucasian populations. Methods Beninese ( n = 111) and Belgian ( n = 121) were genotyped for CYP2C9 * 2 , * 3 , * 4 , * 5 , and * 11 as well as for CYP2C19 * 2 and * 3 . Results The distribution of alleles was: CYP2C9 * 1 : 95.5 vs. 82.2% ( P < 0.001); CYP2C9 * 2 : 0 vs. 10% ( P < 0.001); CYP2C9 * 3 : 0 vs. 7.4% ( P < 0.01); CYP2C9 * 4 : both 0%; CYP2C9 * 5 : 1.8 vs. 0% ( P = 0.05); and CYP2C9 * 11 : 2.7 vs. 0.4% ( P < 0.05). The frequencies of the CYP2C19 * 2 allele were 13 vs. 9.1%, respectively. CYP2C19 * 3 was not detected in either population. The 95% confidence intervals for the differences of frequencies of CYP2C9 * 1 , CYP2C9 * 2 , CYP2C9 * 3 , CYP2C9 * 4 , CYP2C9 * 5 , CYP2C9 * 11 , CYP2C19 * 1 , CYP2C19 * 2 and CYP2C19 * 3 between Belgian and Beninese were 7%, 19%; − 14%, − 6%; − 11%, − 4%; − 1%, 1%; 0%, 4%; 0%, 5%; − 10%, 2%; − 2%, 10%; − 1%; respectively. The distributions of CYP2C9 genotypes in the Beninese and Belgian individuals were: CYP2C9 * 1/ * 1 : 91 vs. 67% ( P < 0.00001); CYP2C9 * 1/ * 2 : 0 vs. 18.2% ( P < 0.0001); CYP2C9 * 1/ * 3 : 0 vs. 11.6% ( P < 0.001); CYP2C9 * 1/ * 5: 3.6 vs. 0% ( P = 0.05); CYP2C9 * 1/ * 11 : 5.4 vs. 0.8% ( P = 0.05); CYP2C9 * 2/ * 3 : 0 vs. 1.6% (NS); CYP2C9*3/*3: 0 vs. 0.8% (NS). The distributions of CYP2C19 genotypes between these ethnic groups were: CYP2C19 * 1/ * 1 : 73.9 vs. 83.5% (NS); CYP2C19 * 1/ * 2 : 26.1 vs. 14.9% ( P < 0.05); CYP2C9 * 2/ * 2 : 0 vs. 1.6% (NS). Conclusions Differences of allele frequencies between Beninese and Belgian populations were statistically significant for CYP2C9 * 2 , * 3 , * 5 and * 11 , but not for CYP2C9 * 4 or for CYP2C19 * 2 and * 3 .