Many studies have been proposed to identify insertion/deletion (InDel) polymorphisms in humans for forensic genetic studies. However, the discriminatory power of InDels is limited by the poor polymorphisms of diallelic markers. To improve their discriminatory power, we developed multi-InDel, a novel autosomal marker comprising more than two InDel loci that are tightly linked by their physical position and combined into a specific marker by a pair of PCR primers. This strategy gives at least three haplotypes for each multi-InDel marker. Such markers can be potentially very useful in forensic applications. In this study, we focused on multi-InDel markers located on X chromosome (ChrX). A multiplex system with 13 multi-InDel markers, including 28 InDel loci in ChrX, was developed. To validate the multi-InDel panel, the haplotype distribution in a population sample and in a set of pedigrees was investigated. This study demonstrates usefulness of these markers for individual identification and relationship studies. We highlight the fact that the multi-InDel markers located on ChrX can provide new supporting information for complex kinship testing.