BACKGROUND: Intestinal metaplasia (IM) is pre-neoplastic with variable cancer risk. Cytosponge-TFF3 test can detect IM. We aimed to 1) assess whether quantitative TFF3 scores can distinguish clinically relevant Barrett's oesophagus (BO) (C≥1 or M≥3) from focal IM pathologies (C<1, M<3 or IM of gastro-oesophageal junction); 2) whether TFF3 counts can be automated to inform clinical practice. METHODS: Patients from the Barett's oEsophagus Screening Trial 2 (BEST2) case-control and BEST3 randomised trials were used. For aim 1, TFF3-positive glands were scored manually and correlated with clinical diagnosis. For aim 2, machine learning approach was used to obtain TFF3 count and logistic regression with cross-validation was trained on the BEST2 dataset (n = 529) and tested in the BEST3 dataset (n = 158). FINDINGS: Patients with clinically relevant BO had higher mean TFF3 gland count compared to focal IM pathologies (mean difference 4.14; 95% confidence interval, CI 2.76-5.52, p < 0.001). The mean class-balanced validation accuracy was 0.84 (95% CI 0.77-0.90), and precision of 0.95 (95% CI 0.87-1.00) for detecting clinically relevant BO. Applying this model on BEST3 showed precision of 0.91 (95% CI 0.85-0.97) for focal IM pathologies with a class-balanced accuracy of 0.77 (95% CI 0.69-0.84). Using this model, 55% of patients (87/158) in BEST3 would fall below the threshold for clinically relevant BO and could avoid gastroscopy, while only missing 5.1% of patients (8/158). INTERPRETATION: Automated Cytosponge-TFF3 gland quantification may enable thresholds to be set to trigger confirmatory gastroscopy to minimize overdiagnosis of focal IM pathologies with very low cancer-associated risk. FUNDING: Cancer Research UK (12088/16893 and C14478/A21047).