Abstract Congenital nephrotic syndrome of the Finnish type (NPHS1, CNF) is an autosomal recessive disease that affects 1:8000 newborns in Finland. NPHS1 is characterised by heavy proteinuria already in utero and typical signs of nephrotic syndrome (NS) are present at or soon after birth. Due to the evident absence of extrarenal symptoms, NPHS1 has been considered a model disease for NS. In this study, the NPHS1 locus on chromosome 19q13.1 was sequenced and analysed with computer programs to identify new genes in the region. Genes were further characterised and sequenced from NPHS1 patient samples, as well as from controls. Analysis of the data resulted in the identification of the affected gene with two mutations that were found to explain 94% of the Finnish NPHS1 cases. The NPHS1 gene was found to encode a novel single-pass transmembrane protein, termed nephrin, which belongs to the immunoglobulin superfamily of cell adhesion molecules. The NPHS1 gene was cloned and recombinant nephrin fragments were produced in prokaryotic and eukaryotic expression systems. These fragments were used to raise antibodies that were utilized to characterise the spatial and temporal expression of nephrin in kidney glomeruli. Nephrin was localised by electron microscopy (EM) in ladder-like structures of the early junctional complexes of developing columnar podocytes at the capillary stage. In mature glomeruli, nephrin was localised to the slit diaphragm (SD) between adjacent glomerular podocyte foot processes. In order to investigate the more general involvement of nephrin in proteinuric disease, its expression was studied in primary acquired NS by immunofluorescence microscopy. The level of nephrin expression was found to be significantly reduced in membranous glomerulonephritis, minimal change disease and in focal segmental glomerulosclerosis. The known effects of nephrin mutations, together with the structure predicted from its sequence and localisation of the protein to the SD, emphasizes its indispensable role in maintaining the integrity of the glomerular filtration barrier. The glomerular basement membrane has long been considered to possess the size-selective filtration property of the filtration barrier. However, the identification of nephrin in the SD, as well as its alterations in proteinuria, has led us to reconsider SD as the final decisive size-selective filter.