At a U19 top level premier game one of the players had only one arm. His other arm was a “stump” extending approximately to just above his elbow.

The issue was that this player due to his disability had a distinctive advantage on the throw-ins particularly in the attacking third.

This player was quite athletic, and had developed the ability with one arm to throw the ball with accuracy from one touch line to the far end of the Penalty area extending out from the far post.

Effectively with his one armed throw-in technique, the team had the equivilent of a direct kick or corner kick on any throw-in.

This player was a very skilled field player, but was able to throw the ball in 50-100% farther than any other player with two hands over the head.

How should a referee, or AR deal with a potential disability issue like this which the team was exploiting his physical characteristics to gain a goal scoring opportunity on every throw-in in the attacking 1/3?

USSF answer (October 7, 2010):
The following excerpt from the USSF publication “Advice to Referees on the Laws of the Game” may prove helpful.

A throw-in must be performed while the thrower is facing the field, but the ball may be thrown into the field in any direction. Law 15 states that the thrower “delivers the ball from behind and over his head.” This phrase does not mean that the ball must leave the hands from an overhead position. A natural throwing movement starting from behind and over the head will usually result in the ball leaving the hands when they are in front of the vertical plane of the body. The throwing movement must be continued to the point of release. A throw-in directed straight downward (often referred to as a “spike”) has traditionally been regarded as not correctly performed; if, in the opinion of the referee such a throw-in was incorrectly performed, the restart should be awarded to the opposing team.  There is no requirement in Law 15 prohibiting spin or rotational movement. Referees must judge the correctness of the throw-in solely on the basis of Law 15.

The acrobatic or “flip” throw-in is not by itself an infringement so long as it is performed in a manner which meets the requirements of Law 15.

A player who lacks the normal use of one or both hands may nevertheless perform a legal throw-in provided the ball is delivered over the head and provided all other requirements of Law 15 are observed.

NOTE: If the one-armed thrower you describe does not fulfill the requirements of Law 15, then his throw-ins are not legal. In addition, some two-armed players can also throw in the ball to prodigious distances.