This work describes the main advantages and the steps involved in the optimization of a multiplex system able to characterize 38 noncoding biallelic Insertion Deletion Polymorphisms (Indels). With this methodology, all markers are amplified in a single PCR, using short amplicons (up to 160 bp) in order to improve its performance in degraded samples. Alleles are easily detected using capillary electrophoresis. The Indel multiplex typing strategy here described has the same desirable characteristics of forensic SNP assays, including genetic markers (a) with low mutation rates, increasing their usefulness in some kinship cases where few or single incompatibilities can be explained by mutation, and (b) that can be typed using a short amplicon strategy, increasing their usefulness in cases where degraded samples are available. Moreover, this approach uses simple and well-established methodologies already applied in forensic STR assays.