After retiring from full-time riding in 1996 following a career as one of the top domestiques of cycling's modern era, Yates briefly worked with the Linda McCartney team before switching to Discovery in 2005.
There, he helped guide Lance Armstrong, with whom he had forged a successful personal relationship in his riding days, to the last of his seven - now rescinded - Tour de France titles.
He then moved on to Team Sky and was seen as a key figure in Bradley Wiggins' triumph in this year's Tour.
Proud
Yates acknowledges there will be rumours surrounding his exit from Team Sky but insists he is exiting the sport for personal reasons.
In a statement released to the Press Association, the 52-year-old said: "The last three years with Team Sky have been fantastic and a highlight of my long career in cycling.
"I'm proud to have been involved with the team at such an incredible time for the sport.
"I have suffered with my health in recent years and have spent a lot of time away from my home so I feel the time is right to focus on myself and my family.
"I realise the timing of my retirement will lead to speculation given what is currently going on in the sport but I can walk away with my head held high knowing I have done nothing wrong."