According to current concepts breast cancer is considered a polygenic disease.Moreover,once breast cancer has occurred treatment outcome of patients receiving systemic therapy is subject to inter-individual variation and therefore unpredictable.Inter-individual variations both with respect to risk and treatment response may have their origin in polymorphisms.To test this hypothesis large-scale association studies (case-control,case-case comparisons) have become popular that investigate a multitude of polymorphic loci for the identification of a potential relevance.Such brute force genotyping tasks are challenged by feasibility,reliability and reasonable costs.This presentation focuses on new generation genotyping methods that may serve current demands in complex diseases and pharmacogenetic research.