Cells persistently infected with prions continuously produce protease-resistant prion protein (PrP-res). Here, we show that the PrP-res level in prion-infected Neuro2a (N2a) neuroblastoma cells decreased to 50% of their initial level over the first 48 h and then recovered by 96 h after seeding. The level of cellular prion protein (PrP(C)) also appeared to fluctuate, but did not influence the fluctuation of the PrP-res level. Prion-infected N2a cells, co-cultured with a higher number of prion-unsusceptible cells, had twice as much PrP-res as those cultured without unsusceptible cells, suggesting that cell density influences the fluctuation of PrP-res as. Direct cell-to-cell contact between cells, rather than soluble factors, was involved in the cell density-dependent increase in the PrP-res level. The cholesterol content, which is known to influence PrP-res formation, also changed depending on cell density. Our data suggest that alterations in cellular microenvironments controlled by cell density influence PrP-res formation.