Peptides have ubiquitous regulatory roles. Preliminary investigations revealed that during the acute phase of relapse in multiple sclerosis (MS), patients had high levels of peptide like compounds in their urine and variable excretion patterns. To substantiate this finding, a larger patient cohort was studied. Urine samples from MS patients equivalent to 250 nano-moles creatinine were fractionated by HPLC (High Performance Liquid Chromatography) and C-18 reverse phase columns. The eluate was monitored at 215, 280 and 325 nanometers. Mass spectroscopy was done off line. Many were analyzed in both quiescent and active phase of their disease. Most MS patients had much higher urine peptide levels during relapse than controls, and their own peptide levels in remission.