As read on the 2 Feb 2008 edition of the Non-Prophets radio show, from Dial-an-Atheist Ohio before that, and partially originally from Frank Zindler, here's the full smallpox version of

Jesus loves the little zygotes

Jesus loves the little zygotes
all the zygotes of the world.
Jesus loves them until they're born
then abandons them forlorn.
Jesus loves the little zygotes 'til they're born.

Jesus loves the little children
all the children of the world.
Jesus gives them heart defects
measles, mumps, and ringwormed necks.
Jesus loves the little children of the world.

Jesus lets their parents beat them,
bruise their bodies black and blue.
Jesus gives them birth defects,
scurvy, ticks, and palette clefts.
Jesus loves the little children of the world.

Jesus gives the children cancer.
Earaches, lice, and scabies too.
Bowel obstructions, altered lips,
blighted brains and twisted hips.
Extra chromosomes to help them when they pray.

Hallelujah.

Jesus gives the children acne.
AIDS and leprosy galore.
Germs and worms of every kind.
Things to make the children blind.
But he cannot give them smallpox anymore.

Scientists and unbelievers
wiped the pox right off the earth.
Jesus still gives gifts to kids,
broken nose and burnt eyelids.
But he cannot give them smallpox anymore.