Summary: When choosing a read mapper, one faces the trade off between speed and the ability to map reads in highly polymorphic regions. Here we report NextGenMap, a fast and accurate read mapper, which reduces this dilemma. NextGenMap aligns reads reliably to a reference genome even when the sequence difference between target and reference genome is large i.e. highly polymorphic genome. At the same time, NextGenMapoutperforms current mapping methods with respect to run time and to the number of correctly mapped reads. NextGenMap efficiently utilizes the available hardware by exploiting multi-core CPUs as well as graphic cards (GPUs), if available. In addition, NextGenMap handles automatically any read data independent of read length and sequencing technology.