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Purpose – The purpose of this paper is to propose an automatic metadata extraction and retrieval system to extract bibliographical information from digital academic documents in portable document formats (PDFs). Design/methodology/approach – The authors use PDFBox to extract text and font size information, a rule-based method to identify titles, and an Hidden Markov Model (HMM) to extract the titles and authors. Finally, the extracted titles and authors (possibly incorrect or incomplete) are sent as query strings to digital libraries (e.g. ACM, IEEE, CiteSeerX, SDOS, and Google Scholar) to retrieve the rest of metadata. Findings – Four experiments are conducted to examine the feasibility of the proposed system. The first experiment compares two different HMM models: multi-state model and one state model (the proposed model). The result shows that one state model can have a comparable performance with multi-state model, but is more suitable to deal with real-world unknown states. The second experiment shows that our proposed model (without the aid of online query) can achieve as good performance as other researcher's model on Cora paper header dataset. In the third experiment the paper examines the performance of our system on a small dataset of 43 real PDF research papers. The result shows that our proposed system (with online query) can perform pretty well on bibliographical data extraction and even outperform the free citation management tool Zotero 3.0. Finally, the paper conducts the fourth experiment with a larger dataset of 103 papers to compare our system with Zotero 4.0. The result shows that our system significantly outperforms Zotero 4.0. The feasibility of the proposed model is thus justified. Research limitations/implications – For academic implication, the system is unique in two folds: first, the system only uses Cora header set for HMM training, without using other tagged datasets or gazetteers resources, which means the system is light and scalable. Second, the system is workable and can be applied to extracting metadata of real-world PDF files. The extracted bibliographical data can then be imported into citation software such as endnote or refworks to increase researchers’ productivity. Practical implications – For practical implication, the system can outperform the existing tool, Zotero v4.0. This provides practitioners good chances to develop similar products in real applications; though it might require some knowledge about HMM implementation. Originality/value – The HMM implementation is not novel. What is innovative is that it actually combines two HMM models. The main model is adapted from Freitag and Mccallum (1999) and the authors add word features of the Nymble HMM (Bikel et al, 1997) to it. The system is workable even without manually tagging the datasets before training the model (the authors just use cora dataset to train and test on real-world PDF papers), as this is significantly different from what other works have done so far. The experimental results have shown sufficient evidence about the feasibility of our proposed method in this aspect.