Introduction The aim of this study was to identify the ultrasound features which are associated with malignancy in subcentimetre thyroid nodules. Methods This retrospective study included 454 thyroid nodules <10 mm in size in 413 patients from 2012 to 2016, which were subjected to fine needle aspiration cytology. Each nodule was classified according to the ultrasound patterns of the 2015 American Thyroid Association guidelines and the high suspicion ultrasound features (solid, hypo-echogenicity, irregular margins, microcalcifications, taller-than-wide, interrupted rim calcifications, and extrathyroidal extension) were identified for evaluation of their diagnostic performance. Results Of the American Thyroid Association high suspicion ultrasound features, univariate analysis showed that hypo-echogenicity (sensitivity 81.6% (95% CI 65.7–92.3%), specificity 50.0% (95% CI 43.4–56.6%)), irregular margins (sensitivity 34.2% (95% CI 19.6–51.4%), specificity 92.2% (95% CI 88.0–95.3%)), microcalcifications (sensitivity 23.7% (95% CI 11.4–40.2%), specificity 91.0% (95% CI 86.5–94.3%)), and taller-than-wide (sensitivity 23.7% (95% CI 11.4–40.2%), specificity 92.2% (95% CI 88.0–95.3%)) were significantly associated with a malignant diagnosis. Amongst the above features, subsequent multivariate analysis identified a combination of hypo-echogenicity and irregular margins as significantly associated with malignancy. Our malignancy rates based on American Thyroid Association ultrasound patterns from benign to high suspicion were 0.0, 8.3, 3.9, 15.7, and 40.4%, respectively. The American Thyroid Association high suspicion ultrasound pattern had a sensitivity of 50.0% (95% CI 33.4–66.7%) and specificity of 84.5% (95% CI 79.2–88.9%). Conclusion The presence of both hypo-echogenicity and irregular margins was significantly associated with malignancy in subcentimetre thyroid nodules in our study. Hence, subcentimetre nodules which are hypoechoic with irregular margins may warrant further follow-up.