SAM/BAM alignment file formats are extensively used in virtually all the laboratories devoted to high-throughput sequencing. However, limited effort has been yet dedicated to the development of SAM/BAM quality reporting tools. To overcome this problem, we developed SAM-Profiler, a multiplatform tool dedicated to the advanced quality reporting of SAM/BAM files. SAM-Profiler performs qualitative analysis of SAM/BAM alignment data in the context of next-generation sequencing. It is implemented in C# and can be run under Windows, Linux and MacOS operative systems. Two versions are available: fully graphical, event-driven software and a command-line tool.SAM-Profiler is able to generate an extensive set of qualitative reports on SAM/BAM alignment data, among them: overall, per-base and per-chromosome read quality, mapping quality, duplicate and coverage analyses, bases distribution, perfect, proper and improper mapping, exonic, intronic, intergenic, 5` and 3` UTR coverage, mismatch distribution profile and CG distribution. In presence of paired-end sequencing experiments our tool is able to automatically report the insert size distribution and to analyze the relative pair mapping, reporting absolute and relative distribution of properly, improperly mapped, mapped/unmapped and unmapped pairs. Its modular architecture allows embedding additional analytical monitoring/reporting tools to the already developed list, allowing SAM-Profiler to grow according to the specific requests of the end-users.