bookmark mtDNA-Server A web server based on Hadoop, allowing to analyze human mitochondrial next-generation sequencing (NGS) data. All aspects from sequence alignment of FASTQ raw data to final results including heteroplasmic variants are covered. By hiding all complex workflow steps, we provide the mitochondrial DNA (mtDNA) research community an easy to use web server, allowing the detection of heteroplasmic variants in a secure and reproducible way. The validation of the integrated heteroplasmy approach shows that mtDNA-Server detects heteroplasmic variants and sample contamination accurately. The within-sample contamination detection based on mitochondrial haplogroups has significant general potential to assess data from whole genome sequencing studies for potential contamination and is therefore not limited to target mtDNA sequencing. mtDNA-Server is conceived to handle large amount of mtDNA NGS data, by taking advantage of parallel data processing using the MapReduce framework, having the main focus on ease of use and reliability of the results to prevent erroneous conclusions.