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Allen  and Prayers for the Soules departed,’ Antwerp, 1565, 8vo. 3. ‘A Treatise made in Defence of the lawful Power and Authoritie of Priesthod to remitte Sinnes: Of the peoples duetie for confession of their Sinnes to Gods ministers:  And of the Churches meaning concerning Indulgences, commonly called the Popes pardons,’ Louvain, 1567, 12mo. 4. ‘De Sacramentis in genere; de Sacramento Eucharistiæ, et Sacrificio Missæ, Antwerp, 1576, 1603, 4to. A work highly esteemed and made use of by Cardinal Bellarmin. 5. ‘An Apologie and true Declaration of the Institution and Endevours of the two English Colleges, the one in Rome, the other now resident in Rhemes, against certaine sinister informations given up against the same.’ Printed at Mounts in Henault (Mons), 1581, 8vo. 6. ‘A briefe Historie of the Martyrdom of 12 reuerend Priests, executed within these twelue Monthes for Confession and Defence of Catholicke Faith, but vnder false Pretence of Treason, a Note of sundrie Things that befel them in their Life and Imprisonment, and a Preface declaring their Innocence,’ 1582, 8vo (anon.). The same work appeared in Latin under the title ‘Brevis Narratio felicis Agonis,’ &c., Prague, 1583, 8vo; and it was translated into Italian with the title: ‘Historia del glorioso Martirio di sedici Sacerdoti martirizati in Inghilterra l'Anno 1581–3,’ Macerata, 1583, 8vo, the accounts of the last four martyrs being added by the translator. ‘Altra edizione, s'è aggiunto il Martirio di due altri Sacerdoti e uno secolaro Inglesi martyrizati l'anno 1577 e 1578,’ Milan, 1584, 8vo; and another edition with still further additions, Macerata, 1584, 8vo. 7. ‘A true, sincere, and modest Defence of the English Catholiques that suffer for their faith both at home and abrode against a false, seditious, and slaunderous Libel, intituled “The Execution of Justice in England.”’ Ingoldstadt, 1584, 12mo (anon.). This reply to Lord Burghley's work appeared also in Latin under the title of ‘Ad persecutores Anglos pro Catholicis domi forisque persecutionem sufferentibus contra falsum, seditiosum, et contumeliosum libellum, inscriptum: Justitia Britannica, vera, sincera, et modesta responsio’ [Douay, 1584], 8vo. 8. ‘The Copie of a Letter written by M. Doctor Allen: Concerning the Yeelding up of the Citie of Dauentrie unto his Catholike Maiestie, by Sir William Stanley, Knight, wherein is shewed both howe lawful, honorable, and neceessarie that action was; and also that al others, especiallie those of the English Nation, that detayne anie townes, or other places, in the lowe countries, from the King Catholike, are bound, upon paine of damnation, to do the like,’ Antwerp, 1587. This letter, of which Latin, Italian, and French translations appeared, was reprinted by the Chetham Society in 1851, with an introduction and notes by Mr. Thomas Heywood. 9. ‘An Admonition to the Nobility and People of England and Ireland, concerninge the present warres, made for the execution of his Holines sentence by the highe and mightie King Catholike of Spaine, by the Cardinal of England. Ao MD.LXXXVIII,’ 8vo. Printed at Antwerp; reprinted at London in 1842 with a preface by Eupater (Rev. J. Mendham). 10. ‘A Declaration of the Sentence of Deposition of Elizabeth, the Usurper and pretensed Quene of Englande,’ 1588. An abridgment of the ‘Admonition.’

Besides writing the above works, he, in conjunction with Dr. Richard Bristow, revised Gregory Martin's English translation of the Holy Scriptures, commonly known as the ‘Douay Bible.’ The New Testament was published at Rheims in 1582, while Allen was there as president of the English College, and the Old Testament at Douay some time after his death, in 1609.

[Fitzherbert, De antiquitate et continuatione Catholicæ Religionis in Angliâ et de Alani Cardinalis vitâ libellus, Rome, 1608, 8vo; Knox's memoir of Allen prefixed to the First and Second Douay Diaries, Lond. 1878, 4to; Letters and Memorials of Cardinal Allen, edited by Fathers of the Congregation of the London Oratory, with an historical introduction by Thomas Francis Knox, D.D., Lond. 1882, 4to (this and the preceding work constitute the first two volumes of the Records of the English Catholics); Dodd's Church History, ii. 44–52, 219–245, iii. 525, and also Tierney's edit. of that work, vols, ii., iii.; Dodd's Apology for the Church History; Strype's Works; Calendars of State Papers; Lingard's Hist. of England, 5th edit. vi. 331, 498, 499, 508, 706; Heywood's preface to Allen's Defence of Sir W. Stanley; Simpson's Life of Campion; Wood's Athenæ Oxon. ed. Bliss, i. 615; Whitaker's Richmondshire, ii. 444; Butler's Book of the Rom. Cath. Church, 259; Pits, Relationes Historicæ de Rebus Anglicis (1619), 792; Petre's Notices of English Colleges; Biog. Brit. under Alan; Fuller's Church History (1655), bk. ix. p. 224: Fuller's Worthies, ed. Nichols, i. 540; Foley's Records, S.J.; MS. Egerton, 2048, f. 1; Godwin De Præsulibus, ed. Richardson, ii. 378; Catholicon, ii. 129; Bartoli, Dell' Istoria della Compagnia di Giesu: L'Inghilterra; Granger's Biog. Hist. of England, 5th edit. i. 270; Jessopp's One Generation of a Norfolk House; Camden's Annales Rerum Angl. et Hibern. regnante Elizabetha, ed. Hearne, 684; Bibl. Grenvilliana; Lodge's Portraits; Edinb. Review, clviii. 354; Wm. Dougal Christie, in Biog. Dict. Soc. D.U.K. ii. 204; Ciaconius, Vitæ Pontificum Romanorum et Cardinalium (1687), iv. 171; Gibson's Lydiate  Rh