The diagnosis is still made in much the same way.  No test has been developed, so a genetic specialist makes the diagnosis, based upon their observations of the physical manifestations.  

Carpenter Syndrome is an inherited autosomal recessive trait.  Each biological parent carries a copy (or two if they have Carpenter Syndrome themselves) of the defective gene.  Carpenter Syndrome has an estimated occurrence rate of approximately one in every one million live births!  With 300 million people in the USA now, that means there are only about 300 cases in the entire country!  The odds of two people who unwittingly carry this defective gene, meeting and reproducing, are astronomical.  

When two carriers procreate, each has a 50/50 chance of passing on the defective gene to the child.  With each pregnancy created by two carriers, there is a 25% chance the baby will have Carpenter's Syndrome.  A 50% chance the baby will be a carrier, but be unaffected themselves, and a 25% chance the child will inherit "normal" copies of gene from each parent (and be completely unaffected), thus ending the cycle.  A person who has Carpenter Syndrome has inherited a copy of the defective gene from each biological parent.  Since they don't have a "normal" copy of that particular gene, they will pass it on to any offspring they produce.  However, unless their mate is also a carrier, their children will be carriers, but otherwise unaffected.

A level 2 ultrasound is often done during pregnancy if fetal abnormalities are suspected.  More often, it seems in these cases, the first sign of anything out of the ordinary, is the craniosynostosis which is obvious at birth.  Craniosynostosis is a medical term which literally means "fused bones of the skull".  The premature fusion of the cranial sutures cause the skull to grow abnormally.  Depending on which sutures are involved, the skull, most commonly, will have either a short (front to back) "cloverleaf" shape (called brachycephaly), or a pointed "cone" shape (called acrocephaly).

Common differences of the facial region includes epicanthal folds ("oriental" looking eyelids), broad cheeks, low set, uneven and malformed ears, flat nasal bridge, small widely spaced teeth that are often late to erupt, wide upturned nose with large nasal openings, an underdeveloped maxilla and/or mandible, and a highly arched and narrow palate which can make speech difficult and contribute to sometimes severe oral aversion and defensiveness.
  
Other physical characteristics associated with Carpenter Syndrome are polydactyly (extra digits), syndactly (webbed or fused digits which develops before 6 weeks, post-conception), and brachydactly (unusually short fingers, sometimes with just a single joint in each).  There are heart defects in about half of the known cases.  A single horseshoe shaped kidney rather than two separate ones, undescended testes in the males, abdominal hernias and rocker bottom feet are not unusual.  

Mild to moderate mental deficiencies are common (about 75% of all cases), but not an obligate feature.  A short, stock stature is also common because of the shortened proximal long bones (of the upper arms and legs, which at birth is sometimes mistaken for dwarfism).