In Step 1 of this 2-step protocol, all patients receive a HAART regimen of nelfinavir (NFV) plus stavudine (d4T) plus lamivudine (3TC). Patients who achieve an acceptable virologic response, defined as 2 consecutive HIV RNA determinations below 500 copies/ml at least 2 weeks apart between Weeks 4 and 16 of Step 1 [AS PER AMENDMENT 10/30/98: defined as 2 consecutive plasma HIV RNA determinations below 50 copies/ml by the Roche Ultrasensitive assay within a 4-week period between Weeks 4 and 24], are randomized to Arm A or B of Step 2. In Arm A, patients receive NFV plus d4T plus 3TC. In Arm B, patients receive NFV plus d4T plus 3TC plus 3 escalating doses of CTX at 6-week intervals. Patients in both arms are followed for at least 52 weeks following randomization to Step 2. During this time, patients undergo blood tests and lymph node biopsies to measure HIV DNA and RNA levels and to characterize the T cell population. Additionally, patients undergo a chest CT of the thymus before randomization to Step 2 and at Week 52 of Step 2. Cerebrospinal fluid may be obtained at Week 52 to determine the amount of HIV RNA and DNA present. [AS PER AMENDMENT 10/30/98: G-CSF is given after the first dose of CTX, at the discretion of the investigator, and after the second and third doses, for up to 14 days, until the absolute neutrophil count is 10,000 cells/mm3. Also, CTX doses may be modified based on pharmacokinetic study results.]