Abstract There is compelling evidence that genetic factors influence several phenotype traits related to physical performance and training response as well as to elite athletic status. Previous case-control studies showed that ∼20 genetic variants seem to be associated with elite endurance athletic status. The present review aims to introduce novel methodological approaches in the field of sports genetics research, which can be applied in the near future to analyse the genotype profile associated with elite athletic status. These include genotype–phenotype association studies using gene expression analysis, analysis of post-transcriptional factors, particularly microRNAs, genome-wide scan linkage or genome-wide association studies, and novel algorithm approaches, such as ‘genotype scores’. Several gaps in the current body of knowledge have been indentified including, among others: small sample size of most athletic cohorts, lack of corroboration with replication cohorts of different ethnic backgrounds (particularly, made up of non-Caucasian athletes), the need of research accounting for the potential role of epigenetics in elite athletic performance, and also the need for future models that take into account the association between athletic status and complex gene–gene and gene–environment interactions. Some recommendations are provided to minimize research limitations in the field of sport genetics.