16Variability in the susceptibility to infectious disease and its clinical manifestation can be determined 17 by variation in the environment and by genetic variation in the pathogen and the host. Despite 18 several successes based on candidate gene studies, defining the host variation affecting infectious 19 disease has not been as successful as other multifactorial diseases. Both single nucleotide variation 20 and copy number variation (CNV) in the host contribute to the host's susceptibility to infectious 21 disease. In this review we focus on CNV, particularly on complex multiallelic CNV that is often not 22 well characterised either directly by hybridisation methods or indirectly by analysis of genotypes and 23 flanking single nucleotide variants. We summarise the well-known examples, such as alpha-globin 24 deletion and susceptibility to severe malaria, as well as more recent controversies, such as the 25 extensive CNV of the chemokine gene CCL3L1 and HIV infection. We discuss the potential biological 26 mechanisms that could underly any genetic association and reflect on the extensive complexity and 27 functional variation generated by a combination of CNV and sequence variation, as illustrated by the 28 Fc gamma receptor genes FCGR3A, FCGR3B and FCGR2C. We also highlight some understudied areas 29 that might prove fruitful areas for further research. 30 31