| No. | Title | Composer | Comments |
| 1. | Lamentations. Heth. Peccatum peccavit | Robert White | (Heth, Teth, Iod, Caph, Lamed, Mem) |
| 2. | Miserere mei Deus | Robert White | |
| 3. | Christe qui lux es et dies, I | Robert White | |
| 4. | Christe qui lux es et dies, II | Robert White | |
| 5. | Christe qui lux es et dies, III | Robert White | |
| 6. | Manus tuae fecerunt me | Robert White | |
| 7. | Portio mea, Domine | Robert White | |
| 8. | Justus es, Domine | Robert White | |
| 9a. | Ne irascaris, Domine | William Byrd | |
| 9b. | Civitas sancti tui | William Byrd | Part 2 of no. 9 |
| 10. | O Domine, adjuva me | William Byrd | |
| 11a. | Tribulationes civitatum | William Byrd | |
| 11b. | Timor et hebetudo | William Byrd | Part 2 of no. 11 |
| 11c. | Nos enim pro peccatis | William Byrd | Part 3 of no. 11 |
| 12. | Domine, exaudi orationem | William Byrd | |
| 13. | Domine, praestolamur | William Byrd | |
| 14. | Ad te clamamus | Christopher Tye | |
| 15. | Omnes gentes, plaudite manibus | Christopher Tye | |
| 16. | Esurientes implevit bonis | John Sheppard | |
| 17. | Angelus ad pastores ait | Orlando di Lasso | |
| 18. | Veni in hortum meum | Orlando di Lasso | |
| 19. | O salutaris hostia | Thomas Tallis | |
| 20. | Salvator mundi, I | Thomas Tallis | |
| 21. | Candidi facti sunt | Thomas Tallis | |
| 22. | Dum transisset Sabbatum | Robert Johnson | |
| 23. | Exaudiat te, Dominus | Robert White | |
| 24. | Tribulationem et dolorem inveni | Alfonso Ferrabosco | |
| 25. | Non me vincat, Deus meus | Nicholas Strogers | |
| 26. | Dum transisset Sabbatum, I | John Taverner | |
| 27a. | Tribulatio proxima est | William Byrd | |
| 27b. | Contumelias et terrores | William Byrd | Part 2 of no. 27 |
| 28. | Appropinquet deprecatio mea | Robert White | |
| 29. | Christus resurgens | John Tailer | |
| 30a. | O quam gloriosum est regnum | William Byrd | |
| 30b. | Benedictio et claritas | William Byrd | Part 2 of no. 30 |
| 31a. | Tristitia et anxietas | William Byrd | |
| 31b. | Sed tu, Domine | William Byrd | Part 2 of no. 31 |
| 32. | Apparebit in finem | William Byrd | |
| 33. | Audivi vocem de caelo | William Byrd | |
| 34. | In resurrectione tua | William Byrd | |
| 35. | Retribue servo tuo | Robert Parsons | |
| 36. | Fac cum servo tuo | William Byrd | |
| 37. | Sive vigilem | William Mundy | |
| 38. | Christe qui lux es et dies, IV | Robert White | |
| 39a. | Deus venerunt gentes | William Byrd | |
| 39b. | Posuerunt morticinia | William Byrd | Part 2 of no. 39 |
| 40. | Domine, tu jurasti | William Byrd | |
| 41. | Exsurge, quare obdormis | William Byrd | |
| 42. | O sacrum convivium | Thomas Tallis | |
| 43. | Salvator mundi, II | Thomas Tallis | |
| 44. | Effuderunt sanguinem | William Byrd | Part 3 of no. 39 |
| 45. | Christe qui lux es et dies | William Byrd | |
| 46. | Laetentur caeli | William Byrd | |
| 47. | Facti sumus opprobrium | William Byrd | Part 4 of no. 39 |
| 48. | Ave Maria | Robert Parsons | |
| 49. | Dum transisset Sabbatum | Roose | |
| 50. | Decantabat populus | Anonymous | |
| 51. | Mirabile mysterium | Alfonso Ferrabosco | |
| 52. | Miserere mei, Deus | William Byrd | |
| 53. | O bone Jesu | Robert Parsons | |
| 54. | Vestigia mea dirige | Nathaniel Giles | |
| 55. | Lord, who shall dwell | Robert White | |
| 56. | The Lord bless us and keep us | Robert White | |
| 57. | O Lord, make thy servant Elizabeth | William Byrd | |
| 58. | Prevent us, O Lord | William Byrd | |
| 59. | How long shall mine enemies | William Byrd | |
| 60. | O that most rare breast | William Byrd | |
| 61. | For thee both kings | William Byrd | Part 2 of no. 60 |
| 62. | The doleful debt | William Byrd | Part 3 of no. 60 |
| 63. | Come to me, grief, for ever | William Byrd | |
| 64. | In fields abroad | William Byrd | |
| 65. | Where fancy fond | William Byrd | |
| 66. | Susanna fair | William Byrd | (1588) |
| 67. | While Phoebus used to dwell | William Byrd | |
| 68. | Why do I use my paper, ink and pen? | William Byrd | |
| 69. | La virginella | William Byrd | |
| 70. | I joy not in no earthly bliss | William Byrd | |
| 71. | Ah, golden hairs | William Byrd | |
| 72. | Lord, in thy wrath reprove me not | William Byrd | |
| 73. | Care for thy soul | William Byrd | |
| 74. | Browning | William Byrd | (instrumental) |
| 75. | Browning | Clement Woodcock | (instrumental) |
| 76. | Miserere | Mallorie | (instrumental) |
| 77. | Ascendo ad Patrem | Jean Maillard | attrib. Tye in MS |
| 78. | Rubem quem | Christopher Tye | (instrumental) |
| 79. | Susanne un jour | Orlando di Lasso | |
| 80. | Madonna somm'accorto | Giacomo Fogliano | attrib. Tye in MS |
| 81. | Pour vous aymer | Philippe van Wilder | |
| 82. | De la court | Robert Parsons | (instrumental) |
| 83. | De la court | Robert Parsons | (instrumental), Part 2 of no. 82 |
| 84. | Je fille quand Dieu | Philippe van Wilder | |
| 85. | In nomine | Robert Parsons | (instrumental) |
| 86. | In nomine, V | William Byrd | (instrumental) |
| 87. | In nomine, I | Nicholas Strogers | (instrumental) |
| 88. | In nomine, III | Nicholas Strogers | (instrumental) |
| 89. | In nomine, II | Nicholas Strogers | (instrumental) |
| 90. | In nomine | John Bull | (instrumental) |
| 91. | In nomine | Robert White | (instrumental) |
| 92. | In nomine "Follow me" | Christopher Tye | (instrumental) |
| 93. | In nomine, I | Clement Woodcock | (instrumental) |
| 94. | If that a sinner's sighs | William Byrd | |
| 95. | If women could be fair | William Byrd | |
| 96. | Prostrate, O Lord, I lie | William Byrd | |
| 97. | Even from the depth unto the Lord | William Byrd | |
| 98. | When I was otherwise than now I am | William Byrd | |
| 99. | In nomine, I | Brewster | (instrumental) |
| 100. | O God, wherefore art thou absent | Anonymous | |
| 101. | When I look back | Robert Parsons | in Tenor partbook only (Mus. 986) |
| 102. | Come Holy Ghost / In nomine | Anonymous | |
| 103. | O Lord of whom I do depend / In nomine | Anonymous | |
| 104. | O Lord, turn not away thy face / In nomine | Anonymous | |
| 105. | When May is in his prime | Anonymous | |
| 106. | May makes the cheerful hive | Anonymous | Part 2 of no. 105 |
| 107. | All ye that live on earth | Anonymous | Part 3 of no. 105 |
| 108. | Ah, alas, you salt sea gods | Richard Farrant | |
| 109. | You gods that guide | Richard Farrant | Part 2 of no. 108 |
| 110. | A doleful deadly pang | Nicholas Strogers | |
| 111. | My little sweet darling | Anonymous | |
| 112. | Ah, silly poor Joas | Anonymous | |
| 113. | In terrors trapped | Anonymous | |
| 114. | The saint I serve | Anonymous | |
| 115. | How can the tree but waste | Anonymous | |
| 116. | Alas, alack, my heart is woe | Anonymous | |
| 117. | Lulla, lullaby, my sweet little baby | William Byrd | (Refrain) |
| 118. | Be still, my blessed babe | William Byrd | (Verse) |
| 119. | O Lord, how vain | William Byrd | |
| 120. | My mind to me a kingdom is | William Byrd | |
| 121. | Who likes to love | William Byrd | |
| 122. | Enforced by love | Robert Parsons | |
| 123. | Mistrust not truth | Anonymous | |
| 124. | The day delayed | Anonymous | |
| 125. | Come tread the paths | Anonymous | |
| 126. | Farewell, my lords | Anonymous | Part 2 of no. 125 |
| 127. | Triumph with pleasant melody | William Byrd | |
| 128. | What unacquainted cheerful voice | William Byrd | Part 2 of no. 127 |
| 129. | My faults, O Christ | William Byrd | Part 3 of no. 127 |
| 130. | Blessed is he that fears the Lord | William Byrd | |
| 131. | Blame I confess | William Byrd | |
| 132. | O Lord, within thy tabernacle | William Byrd | |
| 133. | How shall a young man | William Byrd | |
| 134. | Though Amaryllis dance in green | William Byrd | |
| 135. | La gamba | Vincenzo Ruffo | (instrumental, Mss. 984-6 only) attrib. "Francesco Mocheni" in MS. |
| 136. | Trinitas in unitate | Vincenzo Ruffo | in Tenor partbook only (Ms. 987) |
| 137. | Hey down, sing ye now after me | Anonymous | in Bassus partbook only (Ms. 988) |