Infantile hydrocephalus results in neurological deficits despite surgical treatment. Fetal-onset hydrocephalus in humans can be caused by developmental abnormalities that are genetic in origin. The H-Tx rat has hydrocephalus with 40% penetrance and a polygenic inheritance. A backcross with Fisher F344 inbred strain produced a total of 1500 progeny with 17.5% hydrocephalus. Of these, only 12.3% had overt disease and the remaining 5.2% had mild disease seen only after fixation of the brain. Disease severity was measured for all affected rats using the ratio of ventricle to brain width. The severity measure confirmed that there are two populations, mild hydrocephalus (M; ratio, <0.4) and severe hydrocephalus (S; ratio, >0.4), with a small overlap. For genotyping, the two populations were each subdivided based on the ratio measure to give a total of four groups of increasing severity. After an initial genome scan with microsatellite markers, all hydrocephalic rats and a subset of 128 normal progeny were genotyped on chromosomes 4, 9, 10, 11, 17 and 19. Rats in the mildest group had association with a locus on chromosome 4 (LOD 2.4), whereas those in the severest group were associated with a locus on chromosome 17 (LOD 3.2). All except the least affected group were associated with a heterozygous genotype on chromosomes 10 and 11 (LOD 4.5 and 3.5, respectively). Chromosomes 9 and 19 had weak linkage to hydrocephalus. The number of hydrocephalus-associated loci carried by each rat correlated with the severity of disease. It is concluded that the severity of hydrocephalus in H-Tx is influenced by different genetic loci.