The first has to do with the unintended consequences of...
As is true in most novels, there are multiple themes in The Memory Keeper's Daughter by Kim Edwards; however, two of them are more significant than the others because they are connected to nearly every aspect of the plot.
The first has to do with the unintended consequences of keeping secrets. When his daughter is born and he realizes she has Down's Syndrome, Doctor David Henry thinks he is doing the right thing by getting rid of the baby. This one simple act shapes the lives of two families: his and Caroline's, his nurse.
Caroline's life is forever changed because she cannot bear to leave this helpless baby in an institution, and now she, too, has to keep a secret. She instantly becomes a mother, and she immediately has to uproot her entire life so that her secret will not be revealed and Phoebe will not be taken away from her. For Caroline the secrecy creates fear and distrust, as she is forced to keep someone else's secret as well as her own. Having Phoebe in her life, however, is more than enough compensation for this secretive way of living. Eventually she is able to tell David:
“You missed a lot of heartache, sure. But David, you missed a lot of joy.”
David's family also suffers from this horrible secret David keeps. Though his wife did not consciously know that she had twins, she senses something is not as it should be. Phoebe's twin brother, Paul, also suffers from some kind of inexplicable emptiness because of a loss he senses but cannot name.
David is the one who suffers the most, however, as he is the one who deals with the guilt and shame of abandoning his own daughter. He had his reasons for doing so, of course, but that does not change the reality of having to live with his decision. Instead of the thing he must have hoped would happen by getting rid of Phoebe, which is a heartache-free life unlike his own childhood (with a sick sister who died young), his decision actually causes more heartache than he could have imagined on that snowy night in his clinic. The relationship between David and his wife and son grows aloof at first and bitter later on, all because of the secret David is harboring. That certainly could not have been his intention when he ordered Caroline to do such an unthinkable act.
The second inescapable theme is the lack of understanding about Down's Syndrome. It is an unpreventable condition, but of all the people, a doctor should not have been so quick to simply want to dispose of the problem. This theme of ignorance (lack of understanding) about the disease is a constant presence in the story, from Phoebe's mother Caroline who has to learn what she can as she goes (despite her medical training) to the school system which does not want to have anything to do with Phoebe and any others like her.
No one has adequate information, understanding, or training about Down's Syndrome, and that is a tragedy. We are appalled at the idea that newborn babies with this condition being sent away to institutions, places we know cannot replace a loving, nurturing, inspiring family environment--even if anyone were trying to do that for these children. This lack of understanding lasted far too long in this country, and that is reflected in a trained medical professional being so frightened of the condition that he gave his child away and kept that secret from the child's mother and twin brother. David felt shame, and he should have.
Other themes can be found on the excellent eNotes site, linked below.