Type 1 diabetes mellitus (T1DM) is an autoimmune disease with complex interactions between genetic and environmental factors. We compared antibody levels to various infectious agents and of autoimmune-associated autoantibodies between Colombian T1DM patients, their close family members and healthy controls. Significantly lower levels of antibodies against several infectious agents were detected in the T1DM patients. These included Helicobacter pylori (P = 0.01), cytomegalovirus (P = 0.001), Epstein-Barr virus (P = 0.02) and Toxoplasma (P = 0.001). T1DM patients had significantly higher levels of IgG-anti-gliadin antibodies (P = 0.001) and IgG-antitissue transglutaminase antibodies (P = 0.03), and a borderline association with anticentromere antibodies (P = 0.06). The lower level of antibodies against infectious agents in T1DM patients may be related to their younger ages, but may also point to a protective role of those infections in T1DM development in susceptible individuals. Our results confirm the association between T1DM and celiac disease. A possible association with anticentromere antibody needs further studies.