A herpes simplex virus-type 1 low passage, clinical eye isolate, E-43 at P2, was compared with its variant progeny, SLi-43 at P8, in terms of ocular disease, cytopathic effects, and genomic variation. In New Zealand White (NZW) rabbits, E-43 produced mild epithelial defects and punctate lesions with full recovery by Day 10 postinfection (pi). SLi-43 caused dendritic lesions, progressing to geographic ulceration and death from herpes simplex virus encephalitis in 10 days postinfection. In RK, Hep-2, and Vero cells, E-43 displayed the syn+ phenotype (aggregation and cell rounding); SLi-43 showed the syn phenotype (syncytium formation). DNA digestion profiles of E-43, SLi-43, and isolates from the brains of infected animals showed that the genomic differences map within the terminal repeat of the unique long segment and the internal joint region, specifically in bands B, E, N, and S (Bam HI) and bands M and N (Hind III). Analysis of the DNA of virus recovered from the brain stem of SLi-43-infected, encephalitic rabbits demonstrated that an in vivo selection for neurotropic virions had taken place. Plaque purification of 20 clones from the original E-43 strain showed that one of 20 was the syn phenotype, indicating that the SLi-43 variant was present in the original E-43 isolate and did not develop de novo by rapid mutation. The parent-progeny relationship between E-43 and SLi-43 forms an ideal model in which to compare differences in pathogenicity at the genomic level, and underscores the importance of heterogeneity within a single herpes simplex virus-type 1 wild-type population in terms of variations in ocular disease.