From the Hebrew Scriptures
(Old Testament)

Genesis 2:18-22:
"And the LORD God said, It is not good that the man should be alone; I will make him an help meet for him. ... And the LORD God caused a deep sleep to fall upon Adam, and he slept: and he took one of his ribs, and closed up the flesh instead thereof; And the rib, which the LORD God had taken from man, made he a woman, and brought her unto the man."

In this passage, God is said to have created Eve from one of Adam's ribs, in order to create a companion/helper for him. If Eve had become a FTM transsexual, this would have thwarted God's plan.
 

Deuteronomy 22:5:
"The woman shall not wear that which pertaineth unto a man, neither shall a man put on a woman's garment: for all that do so are abomination unto the LORD thy God."

This verse is perhaps the most ignored passage in the Bible today. Girls and women commonly wear jeans, slacks and other clothing that are essentially identical to the clothing worn by boys and men.

This is the main biblical verse that is often quoted to condemn transsexuality and cross-dressing. (A cross-dresser is typically a heterosexual male who is sexually excited when wearing women's clothes.)

If you believe that a person's gender is defined by their gender identity, then this passage does not pose a problem for transgender persons. A MTF transsexual would be considered a woman and thus eligible to wear women's clothing. However conservatives believe that genetic gender rules; a MTF transsexual is still viewed as a male and thus ineligible to wear female clothing.
 

1 Samuel 16:7:
"... the LORD seeth not as man seeth; for man looketh on the outward appearance, but the LORD looketh on the heart."

This could be interpreted as supporting the acceptance of people who identify as transgender or transsexual. The verse might imply that humans typically observe only a person's physical appearance -- their genetic gender. On the other hand, God observes the person's interior reality -- their perceived gender.

Psalms 139:13-14:
"For thou hast possessed my reins: thou hast covered me in my mother's womb. I will praise thee; for I am fearfully and wonderfully made: marvelous are thy works; and that my soul knoweth right well."

This is a psalm of praise to God who wonderfully and marvelously formed the writer as a fetus in their mother's womb. One's genetic gender is determined at conception; many researchers believe that the brain's gender identity is determined during gestation. This psalm thus appears to be confirmation that a transgender person/transsexual is exactly what God had in mind. Their Gender Dysphoria is specifically designed, natural, and not an accident. Thus, it could be argued from this verse that persons with Gender Dysphoria should be honored and accepted as equal to cisgendered persons.
 

Ecclesiastes 11:5:
"As thou knowest not what is the way of the spirit, nor how the bones do grow in the womb of her that is with child: even so thou knowest not the works of God who maketh all."

This passage notes that humans cannot know how a fetus is formed in the body of a woman. This is a work of God and cannot be fully understood. This might be interpreted as implying that we must accept, value, and support God's handiwork, including newborns formed with a brain gender opposite of their genetic gender.
 

Zechariah 12:1:
"The LORD ... forms the spirit of man within him ..."

This implies that a person's spirit is separate from their body. This leaves open the possibility that God occasionally makes the spirit and body of a person to be of different genders. If this is God's intent, then it presumably should be respected.