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There is increasing evidence that even a small variation in thyroid function, even within the reference range, is associated with adverse clinical outcomes. Furthermore, there exists a substantial interindividual variation of thyroid function even within euthyroid individuals suggesting an individual hypothalamus-pituitary-thyroid (HPT) axis setpoint. Here we assess potential contributions of the HPT axis organ volumes to the variation of thyroid hormones in the general population. Using linear regression models, we analyzed the association of circulating free T3, free T4, and log-transformed TSH levels with hypothalamus, pituitary gland, and log-transformed thyroid volume in a subsample of up to n = 3438 participants from the population-based Study of Health in Pomerania with a mean age 50.6 years, 44.6% female, and a mean TSH 1.38mU/L. Performing cross-sectional analyses at baseline, we observed inverse associations of pituitary volume with free T4 levels ( β = - 0.74 , P = 0.017 , n = 1 , 372 ) and of thyroid volume with TSH levels ( β = - 0.72 , P = 3.1 × 10 - 147 , n = 3 , 430 ), as well as positive associations of thyroid volume with free T3 ( β = 0.11 , P = 1.3 × 10 - 4 , n = 3 , 310 ) and free T4 levels ( β = 0.81 , P = 1.2 × 10 - 18 , n = 3 , 311 ) but observed no association regarding hypothalamus volume (n ≤ 1636). The findings for free T3 and free T4 were supported by longitudinal analyses in a subsample of up to n = 2040 participants with available longitudinal data and a mean follow-up time of 7.3 years. In summary, using data from a population-based sample, we identified associations between pituitary volume and circulating free T4 as well as thyroid gland volume with circulating levels of TSH, free T3, and free T4 contributing to the variation of thyroid hormone levels.