We assessed the immune response induced in multiple sclerosis (MS) patients who had received NBI-5788, an altered peptide ligand (APL) designed from an immunodominant region (83-99) of the neuroantigen myelin basic protein (MBP) (5, 10, or 20 mg subcutaneously weekly for 4 weeks). The mean frequency of NBI-5788-responsive T cells (stimulation index > 3) in MS patients treated with the APL was 35.8 +/- 12.8% (n = 7) compared with a mean frequency of 6.2 +/- 1.3% (n = 7) for the untreated patients. The mean frequency of whole MBP-responsive T cells in MS patients treated with the APL was not significantly different from that of untreated patients (16.4 +/- 5.7% vs 18.0 +/- 6.3%, respectively). NBI-5788-reactive T-cell lines generated from NBI-5788-treated patients exhibited an increased frequency of cross-reactivity with MBP peptide 83-99 compared with NBI-5788-reactive lines from control MS patients. Cytokine secretion by APL-reactive T-cell lines from NBI-5788-treated MS patients was more frequently T-helper 2-like compared with T-cell lines from untreated MS patients. These results demonstrate that subcutaneous administration of a soluble APL based on the MBP peptide 83-99 in MS patients can induce an APL-reactive immune response in which T lymphocytes cross-reactive with the immunodominant neuroantigen MBP secrete anti-inflammatory cytokines. The significant heterogeneity in immune response between individuals indicates the need for clinical laboratory correlation during the course of therapeutic trials.