The study analyzes whether genetic differences (“genetic distances”) help to explain cross-national IQ differences being controlled for environmental factors. Genetic distances are an indicator of evolutionary history and of difference or similarity between populations. Controlled for environmental determinants the relationship between genetic distances and intelligence differences can be interpreted as an effect of genetic factors. Genetic distances were calculated in Y-chromosomal haplogroup frequencies between N = 101 national populations based on k = 27 genetic studies. Correlations and path-analyses with differences in geographical coordinates and the Human Development Index (HDI) as background and control factors revealed a positive impact of genetic distances on cross-national IQ-differences (r = .37, β = .22 to .40). The strongest impact was found for HDI (r = .67, β = .58). Longitudinal differences have no positive effect (r = −.09, β = −.13 to −.26), latitudinal differences have a positive one (r = .37, β = .07 to .21). The positive relationship to latitudinal differences underpins an evolutionary explanation. Chances and limits of this approach (e.g. no intelligence coding genes detected) understanding national differences in cognitive ability and the role of environmental factors are discussed.