Many applications in insect genetics require repeated analyses on individual organisms. These include population genetic and genomics, linkage mapping, molecular systematics and map-based positional cloning. However, using the polymerase chain reaction, a limited number of analyses are possible with DNA isolated from whole bodies or parts of small or preserved specimens. We describe the optimization of a new technique, Multiple Displacement Amplification, for 100-400-fold amplification of whole mosquito genomes. We demonstrate that MDA amplifies genomic DNA directly from an adult leg or from organisms as small as a first instar mosquito larva. Genetic polymorphisms revealed at individual loci are the same whether using the original genomic DNA or MDA DNA as a template.