Background <p>The drug thalidomide, launched as a sedative, is known for its adverse teratogenic effects and the subsequent major health scandal involving inadvertent abortions in pregnant women and birth defects in thousands of children, prior to its withdrawal from the market in 1961. The drug was later repurposed for treating cancer and dermatologic diseases in humans. Preclinical studies conducted prior to the licensing of thalidomide suggested that it was a very safe drug. However, genetic variation in the C-terminal region of the cereblon (CRBN) protein has been shown to explain differences in function and effect of thalidomide between species, demonstrating that thalidomide and derivative drugs are ineffective in mice. Multiple veterinary studies have explored the therapeutic use of thalidomide in dogs with cancer, with few adverse effects being reported.</p> Methods <p>The current study investigated the genetic evidence supporting therapeutic thalidomide use in dogs, based on genetic data from ~ 2000 individuals and tumor-normal sequencing data from different cancer types.</p> Results <p>Our results show that dogs, similar to mice, encode an isoleucine that affects the C-terminal part of the cereblon protein. This alteration has been shown in mice to inhibit binding of neo-substrates and hence diminish the pharmacological effect of thalidomide. We did not find any evidence that mutations in cancer cells alter the <i>CRBN</i> gene in a manner that would make cancer cells sensitive to thalidomide.</p> Conclusions <p>Our data predicts that thalidomide could have a different pharmacodynamic effect in dogs and advocates that the molecular function of thalidomide in dogs should be investigated to characterize potential effect and understand the drug’s therapeutic role in canine cancer patients.</p>