The genome revolution is providing fresh insights into host and parasite genomes, and new tools are becoming available for examining host-parasite interactions at the proteome level. Technologies such as surface-enhanced laser desorption/ionization time-of-flight (SELDI-TOF) mass spectrometry (MS) can be applied to discover biomarkers (alterations in both host and parasite proteomes) associated with parasitic diseases. Such biomarkers can represent host proteins, fragments of host proteins or parasite proteins that appear in body fluids or tissues following infection. Individual biomarkers or biomarker patterns not only have diagnostic utility (e.g. in active disease, prognosis, tests of cure) but can also provide unique insights into the mechanisms underlying host responses and pathogenesis.