Three groups of 5-week-old cesarian-derived, colostrum-deprived pigs were inoculated intranasally with either a high-virulence isolate (VR2385) or a low-virulence isolate (VR2431) of porcine reproductive and respiratory syndrome virus (PRRSV) or with uninfected cell culture and media. Formalin-fixed, paraffin-embedded tissues from pigs euthanatized at 10, 21, and 28 days post-inoculation were examined by in situ hybridization for PRRSV nucleic acid using a digoxigenin-labeled antisense RNA probe approximately 1,000 nucleotides in length. Alveolar macrophages were positive in the lungs of 9/9, 2/2, and 0/2 VR2385-inoculated pigs and 7/9, 1/2, and 2/3 VR2431-inoculated pigs at 10, 21, and 28 days post-inoculation, respectively. More positive cells were detected in lungs from VR2385-inoculated pigs compared to VR2431-inoculated pigs at 10 and 21 days post-inoculation. Positive cells within lymph nodes were tingible body macrophages in germinal centers and macrophages or interdigitating dendritic cells within the paracortical area. VR2385 was detected in the tracheobronchial lymph node (TBLN) and mediastinal lymph node (MLN) of 7/9 and 9/9 pigs at 10 days post-inoculation, but was only detected in the TBLN of 1/2 and 0/2 pigs and in the MLN of 0/2 and 1/2 pigs at 21 and 28 days post-inoculation, respectively. In contrast, VR2431 was detected in teh TBLN and MLN of 5/9 and 2/9 pigs at 10 days post-inoculation and in the TBLN of 0/2 and 1/3 pigs and in the MLN of 0/2 and 0/3 pigs at 21 and 28 days post-inoculation, respectively. There were more positive cells in TBLN and MLN in pigs inoculated with VR2385 at 10 days post-inoculation. Macrophages located at the epithelial-lymphoid interface of tonsilar crypts and within the paracortical areas were positive in tonsils of 9/9, 2/2, and 1/2 VR2385-inoculated pigs and 7/9, 1/2, and 1/3 VR2431-inoculated pigs at 10, 21, and 28 days post-inoculation, respectively. Positive cells in the thymic medulla were multinucleate and were only detected at 10 days post-inoculation in 2/9 VR2385-inoculated pigs and 4/9 VR2431-inoculated pigs. Positive cells within the spleen were few, spindle-shaped, located within smooth muscle trabecula, and only present at 10 days post-inoculation in 3/9 VR2385-inoculated pigs. We conclude that the tissue tropism and distribution of positive cells within tissues is similar for VR2385 and VR2431. However, tissues from more pigs and more cells within tissues were positive in pigs inoculated with VR2385 than VR2431 at 10 and 21 days post-inoculation. These findings indicate that the more virulent isolate VR2385 may replicate better in vivo than the less virulent isolate VR2431. This supports the hypothesis that an increased ability to replicate in vivo contributes to increased virulence of PRRSV.