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Begun in 1990, The Master's Seminary Journal (ISSN #1066-3959) is a publication of the faculty of The Master's Seminary. It is published semi-annually and contains articles dealing with the Biblical text, theology, and pastoral concerns. It also contains reviews of current books and significant articles relating to these issues.

The Master's Seminary Journal continues to expand its influence in evangelical scholarship with recent articles being recognized in other theological journals. The Master's Seminary Journal is indexed and abstracted in all of the leading research tools including: Elenchus Bibliographicus Biblicus of Biblica, Christian Periodical Index, Guide to Social Science & Religion in Periodical Literature, New Testament Abstracts, Old Testament Abstracts, Religion Index One: Periodicals and Book Reviews in Religion.

Four thematic anthologies of past Journal articles have also been published by Kregel Publications. The Master's Perspective Series, includes four volumes to date:

1. The Master's Perspective on Difficult Passages
2. The Master's Perspective on Contemporary Issues
3. The Master's Perspective on Pastoral Ministry
4. The Master's Perspective on Biblical Prophecy

Every spring a special series of Chapel messages, The Faculty Lecture Series, is presented dealing with a specific issue of current theological interest. Since 1998 the fall issue of the journal has been dedicated as a "single topic" issue, presenting those chapel messages in articles where the full breadth of research, quotations, footnotes, and an extensive bibliography could be presented. The special topics dealt with in the journal are as follows:

1. Biblical Sanctification (2010)
2. Atonement: Scripture on Penal Substitution (2009)
3. The Truth About Homosexuality (2008)
4. New Covenant Theology (2007)
5. The Emerging Church Movement (2006)
6. The New Perspective on Paul (2005)
7. Authority and Sufficiency of Scripture (2004)
8. Cessationism (2003)
9. Rapture Issues (2002)
10. The Openness of God Controversy (2001)
11. Major Ethical Issues Facing the Church (2000)
12. Biblical Covenants (1999)
13. Eternal Punishment (1998)

There has also been one other special issue in the history of the journal, A Festschrift in Honor of Dr. Robert L. Thomas, in Spring 1999. Dr. Thomas, longtime professor of New Testament, has served as the Executive Editor of The Master's Seminary Journal since its inception in 1990.