Patients are divided into 1 of 5 groups based on the stage of HIV infection. Patients receive oral stavudine (d4T), lamivudine (3TC), indinavir (IDV), and nelfinavir (NFV) twice daily for 24 weeks. All patients undergo basic blood sampling to follow HIV-1 RNA levels and absolute T cell subset numbers daily for 5 days; then 3 times a week for 3 weeks; 2 times a week for 4 weeks; every 2 weeks for 12 weeks; and monthly thereafter for a total of 3 years. In addition, the following tissues are sampled at baseline and after 2 weeks and 6 months on therapy: 1) lymph node; 2) tonsillar; 3) perirectal lymphoid; 4) cerebrospinal fluid; 5) and semen.