Background and Objectives: Polymyositis and dermatomyositis (PM/DM) are classified as polygenic autoimmune diseases, whereas inflammatory bowel disease (IBD) is considered a polygenic autoinflammatory disease. In the literature, several cases exist reporting the co-occurrence of both conditions. At the molecular level, PM/DM and IBD share common genetic determinants including interferon regulatory factor and vitamin D receptor susceptibility loci. Accumulating evidence underline several indicators that confer poor prognosis in IBD, including antinuclear antibody positivity and the presence of other autoimmune diseases, therefore the aim of this study is to assess the association between these entities. Materials and Methods: This is a population-based retrospective study using data retrieved from a large electronic medical record in Israel, the Clalit health registry. The sample included PM/DM patients and age- and sex-frequency matched controls. The prevalence of IBD in PM/DM was compared between the two groups and logistic regression was applied to control for confounding variables. Predictors of IBD in patients with PM/DM were also explored. Results: Our study included 12,278 subjects with 2085 PM/DM patients and 10,193 age- and sex- frequency-matched controls. The incidence of IBD in patients with PM/DM was significantly higher even after controlling for various confounding variables (OR of 1.73, 95% CI 1.05–2.86, p-value = 0.033). Anti-nuclear antibodies (ANA) positivity was found to be an independent predictor for IBD diagnosis in patients with PM/DM (OR 3.67, 95% CI 1.01–13.36, p = 0.048). Conclusion: Our analysis reports an association between IBD and PM/DM. Such association could point towards a common pathophysiological background. Further research is needed to further describe the clinical courses and whether a unique therapeutic approach is warranted.