Lentiviral gene therapy shows promising results for the treatment of several rare diseases. One important safety aspect is monitoring integration sites in patients over time. Insertional mutagenesis can lead to clonal imbalance and malignant transformation. For some immune disorders like Fanconi anemia, collecting sufficient cell numbers for integration site analysis (ISA) can be challenging. Whole genome amplification (WGA) can help to make these samples accessible for insertion site monitoring. We investigated if WGA alters the integration site repertoire and how it influences the quantification of individual sites. The INSPIIRED pipeline is a ligation-mediated PCR technology using the sonic abundance method to quantify the contribution of individual integration sites. Here, we show ISA results for native and WGA treated genomic DNA of the first WHO lentiviral integration site standard (NIBSC code: 18/144) and a primary murine leukemia clone. WGA had only minor effects on the clonal composition and quantification of individual integration sites.