IMPACT is a completely integrated peak calling tool for ChIP-Seq data which incorporates multi-reads and provides users with high-confidence peaks as well as produces downstream analysis results such as motif discovery, peak-to-gene annotation and associated Gene Ontology functions. We support our computational predictions with validation against independent published qPCR verified sites for all three independent datasets. In particular, we show that IMPACT exhibits high-confidence peaks and stronger biological evidence for the correctness of the identified peaks in the human GABP and NRSF as well as mouse Gata1 ChIP-Seq datasets.