The thymuses from 20 simian immunodeficiency virus (SIV)-infected and 4 uninfected rhesus monkeys were examined at intervals after infection to determine whether there were specific SIV-induced lesions, to document the serial distribution of SIV antigens, mRNA, and DNA, to quantitate the number of infected cells, and to correlate thymic changes with other parameters of infection. The following techniques were used: gross pathology, histopathology, immunohistochemistry, electron microscopy, in situ hybridization, polymerase chain reaction, and limiting dilution culture. Thymic involution due to loss of lymphocytes was apparent 8 weeks after inoculation. No epithelial damage or loss of Hassall's corpuscles was observed. Culture was the most sensitive technique for detecting SIV, being positive in 19 of 20 inoculated monkeys. The polymerase chain reaction was negative in one thymus that was positive at a low level by culture. In situ hybridization was positive in 14 of 19 thymuses examined, with a few macrophages in the cortex having a strong signal and numerous lymphocytes in the medulla having a weak signal. Mature viral particles and viral budding could not be demonstrated by electron microscopy. The number of cells positive for viral RNA by in situ hybridization correlated with the level of serum antigenemia. These observations suggest that thymic macrophages and lymphocytes are infected with SIV within 2 weeks after inoculation. SIV apparently directly causes loss of thymic lymphocytes and immunodeficiency without infecting or damaging the thymic epithelium. No specific SIV-induced lesions were recognized. The number of cells in the thymic medulla expressing SIV RNA correlates with the level of serum antigen, which has been previously shown to be correlated with disease progression.