Recent advancements in machine learning-based multi-label medical text classification techniques have been used to help enhance healthcare and aid better patient care. This research is motivated by transformers’ success in natural language processing tasks, and the opportunity to further improve performance for medical-domain specific tasks by exploiting models pre-trained on health data. We consider transfer learning involving fine-tuning of pre-trained models for predicting medical codes, formulated as a multi-label problem. We find that domain-specific transformers outperform state-of-the-art results for multi-label problems with the number of labels ranging from 18 to 158, for a fixed sequence length. Additionally, we find that, for longer documents and/or number of labels greater than 300, traditional neural networks still have an edge over transformers. These findings are obtained by performing extensive experiments on the semi-structured eICU data and the free-form MIMIC III data, and applying various transformers including BERT, RoBERTa, and Longformer variations. The electronic health record data used in this research exhibits a high level of label imbalance. Considering individual label accuracy, we find that for eICU data medical-domain specific RoBERTa models achieve improvements for more frequent labels. For infrequent labels, in both datasets, traditional neural networks still perform better.