OBJECTIVE: Research on determinants of well-being in patients on thyroid hormone replacement is warranted, since persistent fatigue-related complaints are common in this population. In this study we evaluated the impact of different states of hypothyroidism on fatigue and fatigue-related symptoms. Furthermore the relationship between fatigue and the TSHR-Asp727Glu polymorphism, a common genetic variant of the thyroid stimulating hormone receptor (TSHR), was analysed. DESIGN: A cross-sectional study was performed in 278 patients (140 patients treated for differentiated thyroid carcinoma (DTC) and 138 with autoimmune hypothyroidism (AIH)) genotyped for the TSHR-Asp727Glu polymorphism. METHODS: The multidimensional fatigue inventory (MFI-20) was used to assess fatigue, higher MFI-20 scores indicating more fatigue-related complaints. MFI-20 scores were related to disease status and Asp727Glu polymorphism status. RESULTS: AIH patients scored significantly higher than DTC patients on all five MFI-20 subscales (p <0.001), independent of clinical and thyroid hormone parameters. The frequency of the TSHR-Glu727 allele was 7.2%. Heterozygous DTC patients had more favourable MFI-20 scores than wild-type DTC patients on 4 of 5 subscales. The modest effect of the TSHR-Asp727Glu polymorphism on fatigue was found in DTC patients only. CONCLUSIONS: AIH patients had significantly higher levels of fatigue compared to DTC patients, which could not be attributed to clinical or thyroid hormone parameters. The modest effect of the TSHR-Asp727Glu polymorphism on fatigue in DTC patients should be confirmed in other cohorts.