Astrocytes are indispensable for brain function, yet show signs of age-related impairments. Importantly, these impairments can manifest, as shown in hippocampal astrocytes, in the form of a buildup of hypobranched glycogen molecules, known as polyglucosan bodies (PGBs). Although diseases like adult polyglucosan body disease and Lafora disease link PGBs to cognitive decline, the mechanism and clinical relevance of age-related PGB accumulation remain unclear. In our study of 32 fully sequenced BXD-type mouse strains, we observed a 400-fold variation in PGB burden among 16–18-month-old females. We pinpointed a significant locus, Pgb1, on chromosome 1 (72–75 Mb), which correlated with PGB density, and identified two candidate genes, Smarcal1 and Usp37, harboring variants likely affecting protein function. Additionally, a phenome-wide analysis (~12,000 traits scanned) highlighted Pgb1's influence on Hp1bp3, involved in age-related cognitive changes. However, cognitive tests (conditioned fear memory and Y-Maze tests) across different strains did not show a negative correlation between PGB burden and cognition. Taken together, we have identified a major modifier locus controlling PGB burden in the hippocampus and shed light on the genetic architecture and clinical relevance of this strikingly heterogeneous hippocampal phenotype.