The Special Report team visited grounds from lower leagues to the Premier League last year and although abuse was not widespread, several incidents of vile chanting were recorded.
Many people might think colour and religious discrimination is an isolated issue, but with recent bans for Liverpool's Luis Suarez, Chelsea's John Terry and Serbian U21 players (for the game against England), as well as AC Milan's walk-off at Italian lower division club Pro Patria, racism continues to plague the sport.
Marvin Sordell, the Bolton striker who said he was called a "slave" by Millwall fans in October last year, inspired this latest probe and is one of the few footballers to speak out about his experiences.
The 21-year-old told Sky Sports News in the programme broadcast on Monday night: "We can't be silent. We need to make people aware there is a problem and only when people are aware of it then it can be sorted out."
The investigation visited the home of Leeds United and Birmingham, but did not hear abuse. Blackburn striker Colin Kazim-Richards suffered abuse at Burnley, but a further visit to the Den in London on 18 November encountered racism the programme's cameraman described as the worst he had seen in 35 years.
There were 56 separate incidents of racial abuse by five white men, with Leeds striker El-Hadji Diouf the subject of most of the chants by a small section of Millwall supporters. FIFA president Sepp Blatter was shown the footage and later called for clubs to be relegated if players were found to be racially abused.
Millwall did not follow up the incident with Diouf claiming he hadn't been abused, but after being shown the footage, the club's chief executive Andy Ambler said their investigation would be reopened.
After the programme was broadcast, Millwall released a statement reading: "Everyone at Millwall is deeply shocked and appalled by the footage.
"Millwall has been at the forefront of the battle to eradicate racism from football, being the first in the country to introduce an Anti-Racism Trust, and in spite of the incidents shown in this programme, tremendous strides have been made.
"We operate a zero tolerance policy in which we target, arrest and ban any fan identified displaying racist or abusive behaviour. Now that this new evidence has come to light, Millwall FC has requested that Sky make all footage available to the Police, which they have agreed to do. We will assist in identifying the individuals concerned with a view to the strongest possible action."
Sordell's 13-year-old abuser was banned in November from home matches for "the foreseeable future". It is an encouraging sign that some clubs are dealing with the problem, but there is still clearly more the clubs and the sport can do.
Lord Ousely, Kick It Out chairman, told the programme: "Discrimination is still a factor - football at the top is the status quo", while former Aston Villa and England defender Ugo Ehiogu added: "Until society changes, football will always reflect that."
Special Report also discovered "a generation of black players forced to put up and shut up" and keep quiet on any unsavoury incidents.
Peter Herbert, chairman of the Society of Black Lawyers, has written to the Metropolitan Police demanding an urgent investigation "in light of the appalling racial abuse shown so clearly by the Sky TV".
The Metropolitan Police have subsequently requested a copy of the programme shown on Sky Sports News.
Sordell remains in a tiny minority of players willing to discuss their experiences. He added: "I wouldn't say it shocked me but it surprised me living in a multi-cultural country it can still go on. It does though give me more fire and makes me want to do better and prove people wrong and show them I can rise above it."
The chief superintendent of the Metropolitan Police's Public Order branch, Mick Johnson, says his force is working closely with football clubs at tackling racism.
Johnson said: "It is important that we work with football clubs and the football authorities, including the FA, to ensure that there is no misunderstanding about what constitutes racist language or behaviour and that we work with clubs to educate, encourage and empower supporters to stamp out racism in football.
"Some words which historically have been perceived by some as acceptable cause harassment, alarm or distress to others, and people who use this language could be committing a criminal offence.
"Offensive language, within football chants or otherwise, has no place within football, or indeed in society, and those who engage in such behaviour should be under no illusion that they are committing a crime.
"If it is unacceptable outside football then it is unacceptable inside football. We are working closely with partner agencies and all football clubs to get this message across to their supporters."