Systemic autoimmunity describes a group of detrimental conditions, characterized by loss of immunologic self-tolerance. Pattern recognition receptors (PRR) detect recurrent microbial structures including nucleic acids. Nucleic acid-specific PRRs are not well equipped to discriminate between self and non-self nucleic acids and their aberrant activation leads to autoimmune conditions, driven by chronic activation of the type I interferon (IFN) system. This concept has been established by research on the molecular mechanisms underlying the rare Aicardi-Goutières syndrome (AGS). Loss of function mutations in the gene SAMHD1 cause AGS. SAMHD1 was first described as a deoxyribonucleotide (dNTP) triphosphohydrolase (dNTPase) and its activity is tightly regulated during the cell cycle to ensure the correct cellular supply of dNTPs. Cells decrease SAMHD1 dNTPase activity during S phase where the DNA must be replicated and once the S phase is over, dNTPase activity is restored and the dNTP levels are reduced. Loss of SAMHD1 causes an increase of the cellular dNTP concentration during phases of the cell cycle, a well-known trigger for DNA damage, but its consequences has not been addressed yet thoroughly. Recently, SAMHD1 has been also reported to promote homologous recombination directly at the site of DNA double strand breaks (DSB) upon genotoxic stress. By interacting with the protein CtIP, SAMHD1 helped to coordinate the MRN complex and promotes DSB repair. Loss of SAMHD1 impaired this repair mechanism, causing genome instability. Interestingly, this activity of SAMHD1 has also been recently shown to promote restart of stalled replication forks. Lack of SAMHD1 lead to an increase of stalled replication forks and DSBs. How the different activities of SAMHD1 remain balanced and are activated under specific conditions still remains unknown. Additionally, inactivating mutations in SAMHD1 have recurrently been identified in various types of cancers, raising the question, if the protein might function as a tumour suppressor. However, up to date, no in vivo study has addressed the role of SAMHD1 in preventing DNA damage or cancer development, and its relationship to an uncontrolled type I IFN response. In this work, Samhd1-deficient mice were screened in search for sign of DNA damage and an increase in micronucleated erythrocytes, a hallmark for genome instability, was found in comparison with their littermate controls. This increase was still present upon inactivation of nucleic acid sensing pathways, indicating that it was independent of the status of type I IFN response. HSC competitive transplantation experiments with Samhd1-deficient and control HSCs showed a minor contribution of Samhd1 in maintaining lymphogenesis. Despite these findings, Samhd1-deficient mice do not develop any autoimmune disease nor cancer up to 2 years of observation. Previous reports showed a possible relation between loss of SAMHD1 and p53 activation. We inactivated p53 in Samhd1 ko mice, which resulted in accelerated lethality and an earlier onset of tumour formation when compared with p53 ko mice. However, the underlying molecular mechanisms of both observations remains to be fully elucidated. In contrast to the results with p53, inactivation of DNA mismatch repair (knockout of Pms2) in Samhd1 ko mice, had no effect on the tumour-free survival in comparison with Pms2 ko mice. Inactivation of either p53 or Pms2 in Samhd1 ko mice did not altered the spontaneous type I IFN activation. To understand better the different activities described for Samhd1 – dNTPase and DNA damage-related activities –, the dNTPase-inactivating mutations HD238/239AA were knocked into the endogenous Samhd1 gene using CRISPR/Cas9. Using this mouse model, we found that the mutant Samhd1 protein is rapidly degraded in the proteasome, leading to almost complete absence of Samhd1 in the new mouse strain, as seen in patient with similar mutation in Samhd1. These results demonstrated that in patients with mutations in the dNTPase domain, the phenotype is most likely driven by a complete absence of Samhd1 and only by a selective loss of the dNTPase activity. Our work provides new insights in the understanding of Samhd1 as regulator of DNA damage and establishes new ground for further research on the link between DNA damage and type I IFN response.