Purpose: Our study aimed to examine the molecular profiles of cytologically indeterminate thyroid nodules stratified by American College of Radiology (ACR) Thyroid imaging reporting and data system (TI-RADS) categories and to determine whether certain ultrasonographic features display particular molecular alterations. Methods: We performed a retrospective review of cases from 1/1/2016-4/1/2018. Cases with in-house ultrasound, fine needle aspiration (FNA) Thyroid Bethesda Reporting System for Cytology (TBSRTC) diagnoses, molecular testing, and surgery were included. All cases were diagnosed as TBSRTC indeterminate categories. Ultrasound studies were retrospectively reviewed and assigned TI-RADS scores (TR1-TR5) by board-certified radiologists. Final diagnoses were determined based on the surgical resection pathology. Binary logistic regression analysis was used to study whether demographics, TI-RADS levels and TBSRTC diagnoses were associated with ThyroSeq molecular results. Results: 81 cases met the inclusion criteria. The most common alteration across all TI-RADS categories was RAS mutation (TR2 2/2; TR3 10/19, TR4 13/44, and TR5 8/16), which did not stratify with any particular TI-RADS category. Only TR4 and TR5 categories displayed more aggressive mutations such as BRAF-V600E and TERT. ThyroSeq results were positively correlated with thyroid malignancy when non-invasive follicular thyroid neoplasm with papillary-like nuclear features (NIFTP) was categorized in the malignant category for outcome (OR 6.859; p<0.01), but not in the Thyroid Malignancy category when NIFTP was removed from the malignancy category. Echogenicity scores were found to be negatively correlated with ThyroSeq results in thyroid nodules (OR 0.162; P<0.01). Conclusions: Higher risk molecular alterations tended to stratify with the higher TI-RADS categories.