The list of alterations records every change made by Mark Twain in the manuscript. The only exceptions are the essential corrections that he made as he wrote or reread his work. These fall into six categories: (1) letters or words that have been mended, traced over, or canceled and rewritten for clarity; (2) false starts and slips of the pen; (3) corrected eye skips; (4) words or phrases that have been inadvertently repeated, then canceled; (5) corrected misspellings; and (6) inadvertent additions of letters or punctuation that have been subsequently canceled—for instance, an incorrect “they” or “then” altered to “the,” or superfluous quotation marks canceled at the end of a narrative passage. The first words of chapters appear in this list as Mark Twain wrote them, although they are styled in the text of this edition with a full capital followed by small capital letters.

If an altered reading has been emended, the fact is noted in the entry here. In descriptions of Mark Twain's revisions, use of the word “above” signals that new writing is interlined, while use of the word “over” means that something is written in the same space as the reading it supplants, covering it. The term “wiped out” signifies that Mark Twain obliterated a word by smearing it with his finger. “Follows” and “followed by” are spatial, not necessarily temporal, descriptions. A vertical rule indicates the end of a line in the manuscript.

The manuscript of The Prince and the Pauper, in the Henry E. Huntington Library, San Marino, California, consists of 866 pages, inscribed in three distinct colors of ink with some revision in pencil. In this edition, Mark Twain's writing materials are designated as follows:

Ink 1 is violet, a bright bluish purple. The earliest pages of The Prince and the Pauper were written in this ink. Though it has not been possible to date the pages precisely, they were written sometime before the summer of 1877, perhaps in late 1876.

Ink 2 is dark brownish purple. This ink was used on those pages of the manuscript written from late 1877 through early 1878 and again in the winter and spring of 1880. Ink 2 was also used to revise pages written in ink 1.

Ink 3 is blue. This ink was used for the final portion of the manuscript, from May or June 1880 until its completion on 1 February 1881. It was also used to revise the earlier pages written in inks 1 and 2.

Pencil was used intermittently for revision throughout the manuscript.

The following list identifies the sections of Mark Twain's manuscript according to the color of the ink in which they were originally written. The list of alterations in the manuscript gives a full account of writing materials, including revisions.

		Ink color	MS pages
31.1–35.6	The Prince . . . Venice.	ink 3	1–4
45.1–54.3	I will . . . enough,	ink 2	5–19
54.3–55.15	on the . . . barefooted	ink 3	20–25
55.15–56.20	barefooted . . . tears.	ink 1	26–28
57 title–60.2	CHAPTER 3 . . . last!	ink 2	29–34
60.3–60.30	Tom's . . . before	ink 1	35–37
60.30–65.5	except . . . grounds in	ink 2	38–50
65.5–66.10	his bannered . . . down	ink 1	51–52
66.10–115.23	the road . . . bed.	ink 2	53–176
115.24–117.23	As she . . . Presently	ink 3	177–185
117.23–145.4	while . . . cured."	ink 2	188–255
145.4–145.12	After . . . content."	ink 3	255–256
147 title–169.18	CHAPTER 13 . . . of it.	ink 2	257–317
169.19–169.21	The third . . . little	ink 3	318
169.21–201.10	used . . . for it!”	ink 2	319–414
203 title–342.16	CHAPTER 18 . . . p. 11.	ink 3	415–866

The manuscript of The Prince and the Pauper is something of an exception to Walter Blair's observation that in a manuscript of any length Mark Twain “was fairly sure to use three to six kinds of paper and to change from one kind to another in a seemingly capricious fashion.” In this manuscript Mark Twain's use of five varieties of paper follows a pattern of sorts. Crystal-Lake Mills paper was used for the earliest pages, written in ink 1, and for many of the pages written in ink 2. Three varieties of paper—buff, white laid, and P & P—were used only for pages written in ink 2. White wove paper was used for some pages written in ink 2, but mainly for the pages written in ink 3. A description of the papers follows:

Crystal-Lake Mills (CLM) is white, unwatermarked, wove stationery, ruled horizontally in blue, and torn into half-sheets measuring 20.5 by 12.5 centimeters (8 1/16 by 4 15/16 inches). It is embossed in the upper left corner with a picture of a building and the words “Crystal-Lake Mills.”

Buff is a buff-colored, laid stationery which is torn into half-sheets measuring 19.9 by 12.4 centimeters (7 13/16 by 4⅞ inches) with vertical chain-lines 2.5 centimeters (15/16 inch) apart.

P & P is a white, laid stationery, ruled horizontally in blue, and torn into half-sheets measuring 20.3 by 12.4 centimeters (8 by 4⅞ inches). It has horizontal chain-lines 2.2 centimeters (⅞ inch) apart. A device with the initials “P & P,” often quite faint, is embossed in the upper left corner of some of the pages.

White laid (WL) is a white, laid stationery, ruled horizontally in blue, and torn into half-sheets measuring 20.1 by 12.4 centimeters (7⅞ by 4⅞ inches). It has vertical chain-lines 2 centimeters (¾ inch) apart.

White wove (WW) is a white, unwatermarked, wove stationery, torn into half-sheets measuring 17.8 by 11.5 centimeters (7 by 4½ inches).

The following list identifies Mark Twain's use of each of the five varieties of paper in his manuscript.

		Paper	MS pages
31.1–35.6	The Prince . . . Venice.	WW	1–4
45.1–54.3	I will . . . enough,	CLM	5–19
54.3–55.15	on the . . . barefooted	WW	20–25
55.15–115.23	barefooted . . . bed.	CLM	26–176
115.24–117.23	As she . . . Presently	WW	177–185
117.23–132.4	while . . . affair,	CLM	186–221
132.4–134.6	for a . . . digress.	buff	222–226
134.7–145.6	Hendon's . . . truly,	CLM	227–255
145.6–145.12	for one . . . content."	WW	256
147 title–150.27	CHAPTER 13 . . . trembling	P & P	257–265
150.27–156.5	syllables . . . sorrows."	CLM	266–274
156.6–159.13	Tom . . . ceremony	buff	275–285
159.13–160.3	ceremony . . . heavy	CLM	286–288
160.3–166.3	calamity . . . with	buff	289–310
166.3–169.11	very . . . ended.	CLM	311–316
169.12–18	The larger . . . of it.	P & P	317
169.19–21	The third . . . little	WW	318
169.21–170.10	used . . . Hertford	P & P	319
170.10–174.31	would . . . said—	CLM	320–334
174.32–180.13	"Good . . . power	buff	335–356
180.13–181.8	is departed . . . room and	WL	357
181.8–185.12	have . . . office.	CLM	358–366
187 title–342.16	CHAPTER 17 . . . p. 11.	WW	367–866