Background Autoimmune thyroid diseases (ATDs) can be classified into two basic diseases: Graves’ disease (GD) and Hashimoto’s thyroiditis (HT). Here, we review the effectiveness of laboratory and imaging methods used for the early diagnosis of ATD and draw attention to methods that may improve screening. Methods Retrospective data of 142 patients diagnosed with ATD between January 2010 and December 2015 at our paediatric endocrinology clinic were used. Sociodemographic characteristics, clinical findings, treatments and follow-up data of patients were statistically evaluated. Results Of the ATD cases, 81% (n = 115) were female. The median age was 12.5 ± 3.5 (range 1-17) years and 91% (n = 129) of patients were in puberty. There was a significant positive correlation between the height (standard deviation score) and follow-up time for patients with HT (r = 0.156, p < 0.01). Thyroglobulin antibody (TgAb) positivity was found in 75% (45/60) of females with a positive maternal ATD history (p = 0.045). Thyroid-stimulating hormone (TSH), free triiodothyronine (fT3), free thyroxine (fT4) values were significantly altered during the treatment follow-up period in female patients with GD and HT, while only fT4 values were found to be significantly altered in boys with HT. Conclusion Although GD and HT have similar mechanisms, they differ in terms of treatment duration and remission and relapse frequencies. Ultrasonography (USG) screening is a non-invasive procedure that is suitable for all patients with ATD. Based on our results, TgAb could be useful in the screening of girls with a history of maternal ATD.