Reliable sexing of Iguanas especially when young can be difficult, and in most cases sexing young Iguanas can only be done in certainty by an experienced reptile veterinarian who can tell by an examination called "probing the cloacal vent"
However as they get older and nearer maturity...maybe between 1 and 2 yrs of age, then there are some signs that you can look for to help in sexing

.

Spike.&.Uzi 

In the pictures above one Iguana is male and one is female.
A male Iguana usually has a bigger head, sub tympanic shield (the large scales on the cheeks), spines, dewlap and generally a larger head and appearance altogether, it also has what some people term as brain bumps, these are the large fleshy bumps on the top of the head and behind the eyes, these are far more pronounced in a male, and also the jowls, which is the area around the subtympanic shield, are far more pronounced and puffy sort of inflated in a male but flat in a female.
So from the pictures above it would be obvious that the male is on the left hand side.


Femoral pores are also a good indicator in an adult Iguana (see pictures below)

.

This is the same picture duplicated, but the picture on the right has been digitally altered to give a clearer view of a female Iguanas femoral pores.
In a male Iguana the femoral pores exude a waxy substance clearly seen in this photo, and the Iguana uses this to mark its territory or to lay down scent, and he does this by dragging and almost chalking the waxy substance across the floor or branches.
A female Iguana on the other hand, has no substance growing from the femoral pores, so they look very much smaller and sometimes just like a row of dots or small warts in a female Iguana.
So the femoral pores are found along the inside of the Iguana's thighs and are much more pronounced in a male.


Two final definite differences.

Of course there are two certain indicators that can leave no doubt at all in the owners mind.

One, In the picture above a male Iguana is exposing the hemipenes (A male Iguanas reproductive organs)

Two, If the Iguana is gravid or has laid eggs then that too leaves absolutely no doubt as to the gender.