Hypothyroidism is a prevalent condition that can progress from subclinical to overt forms. Early detection of subclinical hypothyroidism is essential for effective and cost-efficient treatment, as well as for identifying risk factors that may prevent disease progression. While TSH is the standard first-line screening test, its levels can be misleading due to various factors, and thyroid ultrasonography, though useful, has limitations. This article explores the use of 3D-NLS bio-resonance feedback diagnostics for the early detection of subclinical hypothyroidism, focusing on biophysical markers such as Fleindler’s Index (FI), Entropy Index, and Noise/Information Index (NII). The study compares these markers with ultrasound criteria and biochemical parameters, including serum levels of T3, T4, TSH, and anti-TPO. Results indicate that the NLS-3D bio- feedback system effectively evaluates biophysical spectral-entropy parameters, revealing significant differences between the groups studied. The analysis demonstrates that Spectral Entropy Analysis (SEA) parameters are valuable for the early detection of thyroid-related disorders and can be utilized in screening asymptomatic patients.