Insertions and deletions are responsible for gaps in aligned nucleotide sequences, but they have been usually ignored when the number of nucleotide substitutions was estimated. We compared six sets of nuclear and mitochondrial noncoding DNA sequences of primates and obtained the estimates of the evolutionary rate of insertion and deletion. The maximum-parsimony principle was applied to locate insertions and deletions on a given phylogenetic tree. Deletions were about twice as frequent as insertions for nuclear DNA, and single-nucleotide insertions and deletions were the most frequent in all events. The rate of insertion and deletion was found to be rather constant among branches of the phylogenetic tree, and the rate (approximately 2.0/kb/Myr) for mitochondrial DNA was found to be much higher than that (approximately 0.2/kb/Myr) for nuclear DNA. The rates of nucleotide substitution were about 10 times higher than the rate of insertion and deletion for both nuclear and mitochondrial DNA.