Prejudice and intolerance are prevalent themes throughout John Wyndham's The Chrysalids. Even within the book's first opening paragraphs, the reader is alerted to the prejudiced and bigoted opinions of the people within the story. The first quote that I feel illustrates the deeply seated prejudice is the following:
"People in our district had a very sharp eye for the odd, or the unusual, so that even my left-handedness caused slight disapproval. So, at that time, and for some years afterwards, I did not mention it to anyone."
David Strom is narrating to the reader a little bit about himself and his society. It's clear from the above quote that the Waknuk people actively look for differences within their population. Those differences are not celebrated, but looked upon with suspicion. Even David's left-handedness is seen as unnatural.
Also in chapter one, David meets a girl who he will become friends with. Her name is Sophie, and David discovers that she has six toes. In the Waknuk society that is reason enough to kill her or banish her. David is too young to understand and know about this, which is why Sophie's parents ask David to keep it a secret. The reason they give to David is the following:
'If anyone were to find out, they'd — they'd be terribly un-kind to her. We've got to see that that never happens.'
The quote shows prejudice because it illustrates that people will mistreat Sophie simply because she looks different.
The "repentances" that people hang in their houses as decorations further the theme of prejudice in the story. The Strom household prominently displays a sign that says "WATCH THOU FOR THE MUTANT." The entire society is taught to actively seek out and squash any sort of genetic divergence that is too far outside of the "norm."