Background: Crystalline silica is an important cause of serious pulmonary diseases. The relationship between this hazard and various physicochemical parameters of crystalline silica has been studied for more than a century, and the toxic potential of silica is known to be associated with its surface properties. However, no in vivo dataset has yet been accumulated to clarify the relevance of this, especially regarding longer term effects. To provide new insights into these longer term effects, we performed single intratracheal instillation testing of five different crystalline silicas and assessed the time-course changes in pulmonary inflammation, lung burden, and thoracic lymph node loads. The tested silicas were prepared from two commercial products [Min-U-Sil5 (MS5, US Silica Company) and SIO07PB (SPB, Kojundo Chemical)] by using three different pretreatment steps: centrifugation (C), grinding (G), and surface dissolving (D). The five types of silica particles—MS5, MS5_C, SPB_C, SPB_G, and SPB_D—were suspended in purified water and intratracheally instilled into male F344 rats. Bronchoalveolar lavage, lung burden analysis, and histopathological examination were performed 3, 28, and 91 days after instillation.Results: MS5 and MS5_C provoked similar biphasic inflammation that differed in severity: MS5 induced granuloma generation 91 days after instillation, whereas the smaller particles of MS5_C elicited only macrophage aggregation. SPB_C induced severe and persistent inflammation, whereas SPB_G and SPB_D induced only slight and transient acute inflammation. All of the silicas were dose-dependently retained in the lung. Silicas that induced prolonged responses were translocated to the thoracic lymph nodes as early as 28 days after instillation. Those that induced transient inflammation were removed effectively from the lung with very little lymph node retention. No quantitative association was identified between lung retention and physicochemical properties, although common features of the retained materials seemed to be reduced solubility, similar surface properties, and relatively small particle. Conclusion: Our key findings suggest that prolonged silica toxicity occurs through lymph node retention. Although the main drivers of translocation to the lymph nodes have not yet been clarified, we provide in vivo evidence of the contributions of at least silica solubility, surface properties, and particle size.