A spacious epithelium-lined body cavity or coelom, which, as regards its origin, may be regarded as a "syncoelom,"[[117]] surrounds the alimentary canal and separates it from the body wall. From the epithelial walls of the coelom are derived the gonads (ovaries and testes), which in the adult are limited to a single pair; while paired and often segmentally-arranged lateral tubular outgrowths from it (renal tubuli) acquire a glandular character and form the basis of the excretory or kidney system. A special portion of the coelom also surrounds the heart and forms a pericardial cavity, and in some Craniata the genital ducts may be formed from its lining membrane.
There is always a muscular heart, consisting of at least three chambers, a sinus venosus, an auricle and a ventricle, and formed by a modification of the initial portion of the ventral or cardiac aorta of the Cephalochordata. The disposition of the great blood-vessels is based on a common plan in all Craniata, and the blood which circulates in them is red in colour owing to the presence of red, haemoglobin-containing corpuscles in addition to the colourless leucocytes which alone are present in the Cephalochordata. Ductless blood-glands of various kinds (spleen, thyroid, thymus, inter- and ad-renal bodies) are very generally present, and modify in different ways the character of the blood as it circulates through them. Besides blood-vessels there is also a somewhat similar system of lymphatic vessels distributed throughout the organs and tissues of the body, which serves the purpose of re-collecting the fluid portion of the blood that has diffused from the blood-vessels for the nutrition of the tissues, and conveying it back to the blood vascular system. These lymphatics contain lymph, a fluid comparable to dilute blood plasma, in which leucocytes float. In addition to their continuity with the blood-vessels at certain points, the lymphatic vessels may also communicate with the coelom, and hence the Craniata must be included among those somewhat rare exceptions to the general rule that no connexion exists between the series of blood-containing channels and the coelom.
In the excretory system the renal tubuli in the adult Craniata rarely retain their primitive embryonic communication with the coelom, and in no instance have they separate and independent external apertures; on the contrary, by the union of their outer or distal extremities, common efferent ducts are formed, which either open into a "cloaca," or directly on to the exterior of the body near the anus.
In all Craniates the dorsally-placed and tubular central nervous system has its anterior portion enlarged and otherwise modified to form a "brain," while the remaining portion, retaining a simpler and more uniform structure, forms the spinal cord. In the embryo the brain always consists of three successive sac-like enlargements known as the fore-, mid-, and hind-brain, and from these are developed the various parts of the complex adult brain, which in the disposition and mutual relations of its parts conforms to a common plan in all the members of the group. There are at least ten pairs of cranial nerves having their origin from the brain, and, in addition, a varying number of spinal nerves arising from the spinal cord, and as a rule formed in each case by the union of a mainly sensory, ganglionated, dorsal root with a mainly motor, non-ganglionated, ventral root.
The median and usually vestigial, parietal, or pineal eye may sometimes be retained as a functional organ, but there exist in all Craniates, in addition, paired eyes, the sensory portion of which, the retina, is derived as an outgrowth from the first of the primary embryonic brain-vesicles. To these organs of special sense are added a pair of auditory organs, and a pair of olfactory organs, besides, in the lower aquatic Craniates, the peculiar sensory organs of the "lateral line."
The gonads are reduced to a single pair in the adult, although it is possible that they may have a multiple origin in the embryo. Gonoducts for the discharge of the sex-cells are almost invariably present, and may owe their origin either to a change of function on the part of certain kidney-ducts, or to independent evolution from the lining membrane of the coelom. The ova are generally provided with a large amount of nutritive reserve in the shape of food-yolk, and hence the process of segmentation is frequently partial or "meroblastic," but in some groups, in which the ova have less food-yolk, it is complete or "holoblastic." The typical invaginate gastrula stage, which is so striking a feature in the embryonic history of the lower Chordata, occurs also in a few of the lower Craniates, but in most of them it is apt to become masked or modified in various ways by the presence of a superabundant amount of food-yolk.
Functional hermaphroditism is of very rare occurrence in Craniates, and, as in the Cephalochordata, reproduction by budding and the formation of colonies are unknown.
Thus distinguished from other Chordata, the Craniata are divided into six "classes," which may be variously grouped, as the following table shows:—
| Ichthyopsida. Breathing by gills at some period of life. Anamniota No embryonic covering or amnion. Anallantoidea. No embryonic respiratory organ or allantois. |  | I. Cyclostomata. Lampreys and Hag-Fishes. |  | Agnathostomata. Without biting jaws. | ||
| II. Pisces. True Fishes. |  | Gnathostomata. With biting jaws. | ||||
| III. Amphibia. Newts, Frogs, and Toads. | ||||||
| Amniota. Amnion present. Allantoidea. Allantois present |  | Sauropsida. |  | IV. Reptilia. Lizards, Snakes, Turtles, and Crocodiles. | ||
| V. Aves. Birds. | ||||||
| VI. Mammalia. Hairy Quadrupeds. | ||||||
| Ichthyopsida. Breathing by gills at some period of life. Anamniota No embryonic covering or amnion. Anallantoidea. No embryonic respiratory organ or allantois. | I. Cyclostomata. Lampreys and Hag-Fishes. | Agnathostomata. Without biting jaws. | |
| II. Pisces. True Fishes. | Gnathostomata. With biting jaws. | ||
| III. Amphibia. Newts, Frogs, and Toads. | |||
| Amniota. Amnion present. Allantoidea. Allantois present | Sauropsida. | IV. Reptilia. Lizards, Snakes, Turtles, and Crocodiles. | |
| V. Aves. Birds. | |||
| VI. Mammalia. Hairy Quadrupeds. | |||