The map gives clues about what makes humans distinct from other animals, and when disorders like autism first take root, researchers said.
"This is another installment in our suite of brain atlases to try to map how all genes are used across the brain and across development," said study leader Ed Lein, a neuroscientist at the Allen Institute for Brain Science in Seattle.
The institute has previously developed maps of the developing and adult mouse brain, the developing monkey brain, and the adult human brain.
The new map is the first to look at the developing human brain - specifically, the developing neocortex, the seat of higher cognitive functions, Lein told 'LiveScience'.
The map is precise enough that scientists can use it to study different types of cells at various stages of development, he added.
Researchers created the map using healthy prenatal brains from a brain bank - a collection of donated human brains. The team used brain tissue with no known abnormalities or viruses such as HIV.
Researchers took snapshots of brains at two different stages of prenatal development.
To measure gene activity, the researchers used a powerful tool known as a DNA microarray, which yields a quantitative measurement of the activity of every gene in the human genome simultaneously - about 20,000 genes in total.
The team compared these gene activity results with data from other species, in particular, the mouse brain.
Researchers found some genes that were turned on in the developing human brain but not in the mouse's brain, or vice versa.
For example, the developing human brain contains genes that are more active in the frontal cortex than in the corresponding part of the mouse brain. The frontal cortex is linked to personality and decision-making.
The map of a healthy developing brain also provides clues to the origin of developmental disorders such as autism, the researchers said. Other studies have revealed certain genes that are active in autism.
Lein's team saw these genes were turned on in newly generated excitatory neurons (which activate other neurons) in the prenatal cortex, suggesting autism may start in the womb, as opposed to later in life.
The findings are published in the journal Nature.