Initially, most eukaryotic sequence projects were devoted to typical animals, fungi and plants. Now more and more effort is put into sequencing protist genomes. Protists are an artificial assemblage containing mostly unicellular eukaryotes from different phylogenetic lineages, and are much more diversified and widespread than higher Eukaryota. Sequenced protist genomes are essential for reconstructing the Tree of Life and understanding significant events in eukaryotic evolution and diversification. Many protists are parasites and pathogens with medical and economic significance, while others play important ecological roles as primary producers and crucial links in food webs. A number of protists also serve as model organisms in various biological fields and are becoming important in biotechnology. Thirty-seven protist genomes were published by the beginning of 2010 and 217 projects are ongoing. Knowledge coming from these projects will be helpful in developing more efficient protection from pathogenic protists and their effective elimination. Sequenced genomes of ecologically important protists could help to understand key environmental phenomena and even to control them. Newly sequenced protist genomes encode previously unknown enzymes and metabolic pathways, which will be useful in further development of biotechnology.