Squick: The descriptions of the surgery Pepys underwent in 1657 to remove a bladder stone will set your teeth on edge.
Medical experts who have read the diary, in particular the parts including Pepys's sympathetic descriptions of his wife's health troubles, conclude that she suffered from Bartholin's cysts. (You can look it up on That Other Wiki, but be aware — the included photograph is Not Safe for Work.)
The surgeon's own papers show that he'd very recently purchased a new operating knife, and Pepys was probably the first person he used it on. At the time, knives were never sterilised; this, then, is probably why Pepys had a good recovery.
Tear Jerker: Elisabeth Pepys' untimely death at age twenty-nine in 1669. Samuel never remarried.
Values Dissonance: Pepys casually mentions things like beating up his household servants.