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Miscellaneous hierarchist Web sites, blogs, and articles will number Origen among the patristic witnesses who said Junia was a man. For just one example, see this 2007 article by David W. Jones, available at the Council on Unbiblical Manhood and Womanhood:
“[Stanley J.] Grenz tentatively mentions that biblical commentators up until about 1200 were in large agreement that Junia was a woman, and according to him, Origen (c. 185-254) assumed that Iounian referred to a woman. Grenz provides no quote from Origen, however, but merely a citation. This is noteworthy, because the actual text in Epistolam ad Romanos Commentariorum 10.26; 39 says the very opposite of what Grenz suggests. The form of the name is nominative masculine singular in Latin, which demonstrates that Origen understood the person mentioned in Rom 16:7 to be a man. This fact alone calls into question the impression given by both Grenz and [Ruth A.] Tucker that it wasn’t until much later that commentators took Iounian to be masculine. . . .
“[As Greek church fathers,] the testimonies of Origen, Epiphanius and Chrysostom must be weighed most heavily: Origen, because he is the earliest of the three exegetes, and the latter two because they are the first ones in extant Greek literature to refer to the name after Romans was written.”
I’ll address Epiphanius (who, in actuality, left no extant commentary on Junia) in a future post. For now, we turn to Origen.
So, did Origen say that the Junia of Romans 16:7 was a man?
The short answer to this question is . . .
The more nuanced answer to this question is . . .
The best manuscript evidence suggests that Origen said Junia was a woman.
The full answer to this question is . . .
Latin has six common declensions for its nouns and proper names (nominative, genitive, dative, accusative, ablative, vocative), Greek has five (nominative, genitive, dative, accusative, vocative). Vocative was a form of direct address and seldom used of biblical figures in ancient commentaries, so it’s not relevant here. Hierarchists like to point out that there are masculine –as or –ας names (Matthias, Ἀκύλας, etc.), and that these names are declined the same as feminine names in their genitive, dative, accusative, and (if applicable) ablative forms, so when a commentator uses a non-nominative case, without any other gender-identifying words, they insist that we cannot know for sure whether a man or a woman is intended.
This amounts to little better than lexical sophistry. When a New Testament figure is called by a very-common masculine name or a very-common feminine name, we always assume that the common name was the author’s intention. It doesn’t matter that Paul only references Junia in the accusative, and that Greek masculine –as names are declined the same as feminine –a names; “Junias” is not a known masculine –as name. Junia is, quite literally, the only person in the New Testament to possess a name that was common and particular to one gender in her day, yet have her gender questioned and frequently reversed based on hypothetical nicknames for the opposite sex that are not known to have existed.
Besides, even if a masculine –as / –ας name is declined the same as a feminine –a / –α name, it just so happens that there were feminine –ας names in Greek: the biblical Dorcas (Δορκας), Pallas (Παλλας), Olympias (Ὀλυμπιας), etc. As long as we’re positing made-up names, this hypothetical “Junias” still isn’t necessarily masculine.
But let’s return to Origen. As I elaborated on in my previous post, Origen mentioned Junia by name five times, and his Greek text was translated into Latin and preserved by Rufinus. Of these five mentions, two were accusative, one was ablative, and two were nominative. So, for these two nominative mentions, did Rufinus write “Junia” or “Junias”?
He wrote “Junia.” All of our earliest and best manuscripts have “Junia” or the (also feminine) “Julia.” Likewise, Hraben of Fulda (also known as Rabanus Maurus), writing in the eighth century, quoted Origen and used “Junia.” 
So why do people claim Origen said Junia was a man?
(1) Four later variant manuscripts (one from the 11th century, two from the 12th century, and one from the 15th century) have the masculine “Junias” here. 
(2) The Patrologia Graeca—an enormous collection of writings of the early church fathers compiled in the 19th century—used “Junias.”
Neither of these are compelling reasons to overturn the earlier (and better) manuscript evidence of a feminine “Junia” in the text. It’s seldom the case in textual criticism that later variants are given precedent over earlier witnesses, unless there is a good reason to believe those later manuscripts are preserving an independent tradition. “I really want Junia to be a man and not a woman” is not compelling evidence of an independent tradition.
And while the Patrologia Graeca can be a good starting point for researchers, the text contains many errors and is “notoriously corrupt.” It should be used with caution. 
One final point
Michael H. Burer and Daniel B. Wallace’s 2001 article, “Was Junia Really an Apostle?,” has become a staple in anti-Junia arguments ever since its publication in 2001. I’ve engaged many hierarchists who clung to it like a binky, unable to analyze its contents for themselves but insisting that it effectively ends the debate on whether Junia was an apostle.
What makes this strange is that Burer and Wallace acknowledged that the best evidence has Origen calling Junia a woman. They wrote:
“Origen seems to cite the name once as masculine and once as feminine, though the masculine is most likely a later corruption of his text.”
Then elaborated in a footnote:
“Junia occurs in In epistola ad Romanos 10.21 (PG 14.1280) , but Junias occurs in 10.39 (PG 14.1289). Rabanus Maurus in In epistola ad Romanos (PL 111.1607-08) cites Origen, In epistola ad Romanos 10.39, but uses the feminine form. Because of this some have asserted that Origen’s text here is corrupt. Moo notes that Rufinus’s translation of Origen’s commentary in PG 14.1281B and 1289A reads a masculine name. ‘But Migne’s text (notoriously corrupt) is probably in error; Origen apparently read a feminine name here . . .’ (D. J. Moo, The Epistle to the Romans [NICNT; Grand Rapids: Eerdmans, 1996] 922).” 
In case you’re wondering how far into the article you have to go to find what I just quoted: it’s on the first and second pages.
So, there ya go. Many of the people claiming that Origen said Junia was a man and that Junia is a non-apostle are, by and large, referencing an article that they didn’t even bother to read.
I agree with David W. Jones and the Council on Unbiblical Manhood and Womanhood. The witness from Origen is among the most significant and should be given considerable weight. And when Origen says that Junia was both a woman and an apostle, we should believe him.
The Junia Series – Introduction
- Who is Junia? A Brief Overview
II. The Patristic Commentators
- Origen on the Apostle Junia
- Did Origen say Junia was a man?
- John Chrysostom on the Apostle Junia
- Rufinus and Jerome on the Apostle Junia
- Ambrosiaster and Theodoret on the Apostle Junia
III. Later Commentators
- Index Discipulorum: A Troubled Witness
IV. Junia: An Apostle Herself, or Just Well-Regarded By Them?
- An Overview of the Burer-Wallace Contention
- Junia and the Island of Tyre
More will be added to the index as the series develops . . .
 Michael H. Burer and Daniel B. Wallace, “Was Junia Really an Apostle?: A Reexamination of Rom 16.7,” New Testament Studies 47 (2001): 76-77, esp. fn3.
 See my previous post in this series, “Origen on the Apostle Junia: A New Translation.”
 Note that Burer and Wallace have made a minor mistake here. The “Junia” that appears in PG 14.1280 (In epistola ad Romanos 10.21) is ablative, not nominative, and a masculine ablative Latin –as name is indistinguishable from a feminine ablative –a name (both masculine and feminine will appear as –a in the ablative case). Rather, as Moo noted, the nominative appears in PG 14.1281 (In epistola ad Romanos 10.26) and PG 14.1289 (In epistola ad Romanos 10.39), but the “corrupt” PG text incorrectly uses the masculine in both places. See my translation of Origen’s comments on Junia for some notes on which cases appear and where.