Purpose: Canine X-linked progressive retinal atrophy 1 (XLPRA1) caused by a mutation in retinitis pigmentosa (RP) GTPase regulator (RPGR) exon ORF15 showed significant variability in disease onset in a colony of dogs that all inherited the same mutant X chromosome. Defective protein trafficking has been detected in XLPRA1 before any discernible degeneration of the photoreceptors. We hypothesized that the severity of the photoreceptor degeneration in affected dogs may be associated with defects in genes involved in ciliary trafficking. To this end, we examined six genes as potential disease modifiers. We also examined the expression levels of 24 genes involved in ciliary trafficking (seven), visual pathway (five), neuronal maintenance genes (six), and cellular stress response (six) to evaluate their possible involvement in early stages of the disease. Methods: Samples from a pedigree derived from a single XLPRA1-affected male dog outcrossed to unrelated healthy mix-bred or purebred females were used for immunohistochemistry (IHC), western blot, mutational and haplotype analysis, and gene expression (GE). Cell-specific markers were used to examine retinal remodeling in the disease. Single nucleotide polymorphisms (SNPs) spanning the entire RPGR interacting and protein trafficking genes (RAB8A, RPGRIP1L, CEP290, CC2D2A, DFNB31, and RAB11B) were genotyped in the pedigree. Quantitative real-time PCR (qRT-PCR) was used to examine the expression of a total of 24 genes, including the six genes listed. Results: Examination of cryosections from XLPRA1-affected animals of similar age (3–4 years) with different disease severity phenotype revealed mislocalization of opsins and upregulation of the Müller cell gliosis marker GFAP. Four to ten haplotypes per gene were identified in RAB8A, RPGRIP1L, CEP290, CC2D2A, DFNB31, and RAB11B for further assessment as potential genetic modifiers of XLPRA1. No correlation was found between the haplotypes and disease severity. During mutational analysis, several new variants, including a single intronic mutation in RAB8A and three mutations in exon 3 of DFNB31were described (c.970G>A (V324I), c.978T>C (G326=), and c.985G>A (A329T)). Expression analysis of stress response genes in 16-week-old predisease XLPRA1 retinas revealed upregulation of GFAP but not HSPA5, DDIT3, HSPA4, HSP90B1, or HIF1A. Western blot analysis confirmed GFAP upregulation. In the same predisease group, no significant differences were found in the expression of 18 selected genes (RHO, OPN1LW, OPN1MW, RLBP1, RPGRORF15, RAB8A, RPGRIP1L, CEP290, CC2D2A, DFNB31, RAB11B, CRX, RCVRN, PVALB, CALB1, FGFR1, NTRK2, and NTRK3) involved in neuronal function. Conclusions: Lack of association between haplotypes of RAB8A, RPGRIP1L, CEP290, CC2D2A, DFNB31, and RAB11B and the disease phenotype suggests that these genes are not genetic modifiers of XLPRA1. Upregulation of GFAP, an established indicator of the Müller cell gliosis, manifests as an important early feature of the disease.