A broad range of genetic and non-genetic factors can lead to kidney injury that manifests as focal segmental glomerulosclerosis (FSGS), which can be classified into primary (idiopathic) and secondary forms. Previous genetic approaches to familial or sporadic cases of FSGS or steroid-resistant nephrotic syndrome identified causal mutations in a subset of genes. Recently, next-generation sequencing (NGS) approaches are becoming a part of a standard assessment in medical genetics. Current knowledge of the comprehensive genomic information is changing the way we think about FSGS and draws attention not only to identification of novel causal genes, but also to potential roles for combinations of mutations in multiple genes, mutations with complex inheritance, and susceptibility genes with variable penetrance carrying relatively minor but significant effects. This review provides an update on recent advances in the genetic analysis of FSGS and highlights the potential as well as the new challenges of NGS for diagnosis and mechanism-based treatment of FSGS.