Background Relation extraction is a fundamental task for extracting gene-disease associations from biomedical text . Existing tools have limited capacity, as they can extract gene-disease associations only from single sentences or abstract texts . Results In this work, we propose RENET2, a deep learning-based relation extraction method, which implements section filtering and ambiguous relations modeling to extract gene-disease associations from full-text articles . We designed a novel iterative training data expansion strategy to build an annotated full-text dataset to resolve the scarcity of labels on full-text articles . In our experiments, RENET2 achieved an F1-score of 72.13% for extracting gene-disease associations from an annotated full-text dataset, which was 27.22% , 30.30% and 29.24% higher than the best existing tools BeFree, DTMiner and BioBERT, respectively . We applied RENET2 to (1) ~1.89M full-text articles from PMC and found ~3.72M gene-disease associations; and (2) the LitCovid articles set and ranked the top 15 proteins associated with COVID-19, supported by recent articles . Conclusion RENET2 is an efficient and accurate method for full-text gene-disease association extraction . The source-code, manually curated abstract/full-text training data, and results of RENET2 are available at https: //github.com/sujunhao/RENET2.