Investigation of cancer cell lines is important for oncology research to characterize and understand mechanisms of cellular signaling and survival strategies in cancer. We analyzed the mutational profile of 11 diffuse large B-cell lymphoma (DLBCL) cell lines using a customized high throughput sequencing panel. We compared our data to previously published mutation data to better characterize these cell lines and establish consensus on the mutational status of some functionally relevant genes. With our targeted sequencing approach we detected 61 somatic mutations. The most frequently affected gene was TP53. MYD88 mutations were only seen in activated B-cell like cell lines. Overall comparison across different datasets revealed that just around 38% of mutations are reliable and can be validated by at least two independent observations whereas 24% of mutations could not be validated. Our analysis reveals considerable discrepancies regarding the mutational profile of some well-established cell lines.