Circadian organization means the way in which the entire circadian sys
tem above the cellular level is put together physically and the princi
ples and rules that determine the interactions among its component par
ts which produce overt rhythms of physiology and behavior. Understandi
ng this organization and its evolution is of practical importance as w
ell as of basic interest. The first major problem that we face is the
difficulty of making sense of the apparently great diversity that we o
bserve in circadian organization of diverse vertebrates. Some of this
diversity falls neatly into place along phylogenetic lines leading to
firm generalizations: i) in all vertebrates there is a ''circadian axi
s'' consisting of the retinas, the pineal gland and the suprachiasmati
c nucleus (SCN), ii) in many non-mammalian vertebrates of all classes
(but not in any mammals) the pineal gland is both a photoreceptor and
a circadian oscillator, and iii) in all non-mammalian vertebrates (but
not in any mammals) there are extraretinal (and extrapineal) circadia
n photoreceptors. An interesting explanation of some of these facts, e
specially the differences between mammals and other vertebrates, can b
e constructed on the assumption that early in their evolution mammals
passed through a ''nocturnal bottleneck''. On the other hand, a good d
eal of the diversity among the circadian systems of vertebrates does n
ot fall neatly into place along phylogenetic lines. In the present rev
iew we will consider how we might better understand such ''phylogeneti
cally incoherent'' diversity and what sorts of new information may hel
p to further our understanding of the evolution of circadian organizat
ion in vertebrates.