One characteristic of autoimmune diseases (ADs) is the production of autoantibodies for extractable nuclear autoantigens, which may aid in the discrimination of the different types of autoimmune diseases and is related to different antinuclear antibody (ANA) patterns. The present study verified the profile of patient samples tested for extractable nuclear antigens (ENA) antibodies in a public hospital and correlated the ENA results with ANA patterns and patient diagnoses. The study reviewed data in the medical records of patients who underwent anti-ENA tests at a public hospital in the West of the State of Paraná from February 2011 to January 2017. Patients were classified according to age, ethnicity, gender, anti-ENA test results, ANA results, and the presence or absence of AD. Thirty-six (20.9%) samples of the 172 anti-ENA tests were positive, seven (4.1%) samples were undetermined, and 129 (75%) exhibited negative results. The ANA reagent was found in 84.3% of the anti-ENA-positive samples. The anti-SSA/Ro autoantibody exhibited the highest frequency in the group, 41.7% (15/36). The most common pattern was nuclear fine speckled, which was found in 24.3% of the samples. The association results indicated a significant relationship between ANA titer and diagnosis in the anti-ENA- and ANA-positive patients. The anti-ENA-negative patients were diagnosed with an AD in 35% (45/129) of the cases, and 75% (27/36) of the anti-ENA-positive patients were diagnosed with an AD. Systemic lupus erythematosus and scleroderma were the most common pathologies in the antigen-positive patients. The anti-ENA test is a good marker to aid in the complex clinical diagnosis of patients with autoimmune diseases.