To identify the prevalence of C. albicans in primary endodontic infections of type two diabetes mellitus (T2DM) patients and compare their clinical and radiographical characteristics with a non-diabetic control group, establishing the possible relationship between primary endodontic infection, T2DM, and C. albicans , since diabetes mellitus (DM), influences the development, course, and response to the treatment of apical periodontitis, but the presence of Candida albicans ( C. albicans ) has not been considered before. A total of 120 patients were selected and divided into two groups: 60 T2DM diagnosed patients and 60 non-diabetic controls. A clinical examination and radiographic analysis were performed to establish a periapical index score (PAI). Root canal samples were taken. Deoxyribonucleic acid (DNA) was extracted, and specific primers were used to identify C. albicans by polymerase chain reaction (PCR) . A twofold increase in the prevalence of C. albicans in T2DM patients was observed in contrast to control patients ( p  = 0.0251). Sixty-five percent of T2DM patients with positive C. albicans scored a ≥ 3 PAI, while only 27% of the patients without C. albicans had a ≥ 3 PAI score ( p  = 0.0065). Long-term DM patients presented C. albicans more frequently ( p  < 0.0001). In this study, long-term T2DM patients carried C. albicans in their root canals more frequently when having a primary endodontic infection. Furthermore, this C. albicans presence seems to be related to a higher frequency of apical periodontitis.