Expert Analysis of official statistics obtained from the Iran Ministry of the Interior, by the Chatham House NGO reveals:
• votes cast exceeded the number of eligible voters in two provinces.
• claims that Ahmadinejad swept the board in rural provinces flies in the face of previous results.
• The plausibility of Mr Ahmadinejad's claimed victory is called into question by figures that show that in several provinces he would have had to attract the votes of all new voters, all the votes of his former centrist opponent, and up to 44% of those who voted for reformist candidates in 2005.
• Irregularities are found in conservative Mazandaran and Yazd provinces where votes cast exceeded the number of eligible voters.
The massive increase in rural votes for Ahmadinejad is not consistent with previous election results and the voting patterns of the ethnic minorities that live in those regions.

There was a strong negative correlation between the percentage of rural voters and the number of votes for Ahmadinejad in the last election. Lorestan is the home province of the most liberal candidate, Medhi Karoubi. This rural province did not voted conservativein the past.
"The numbers from Ilam, Lorestan and Hormozgan almost defy belief," said Thomas Rintoul, one of the researchers.
From the PDF of the complete report published by Chatham House
and the Institute of Iranian Studies,University of St Andrews.
This data supports the contention of academic experts on rural Iranian politics that rural voters have not been the dedicated Ahmadinejad supporters occasionally described in western media. This is supported by the fact that much of Iran’s rural population is comprised of ethnic minorities: Lors, Baluch, Kurdish, and Arab amongst others. These ethnic minorities have a history bothof voting Reformist, and of voting for members of their own ethnic group. Indeed, they were an important segment of Khatami’s vote in 1997 and 2001 and voted largely for Karrubi and Mostafa Moin in 2005.
However, the 2009 data suggests a sudden shift in political support, with
precisely these rural provinces, which had not previously supported
Ahmadinejad or any other conservative (Fig.5) showing substantial swings to Ahmadinejad (Fig.6). At the same time, the official data suggests that the vote for Mehdi Karrubi, who was extremely popular in these rural, ethnic minority areas in 2005 has collapsed entirely, even in his home province of Lorestan, where his vote has gone from 440,247 (55.5%) in 2005 to just 44,036 (4.6%)in 2009. (my bold) This is paralleled by an overall swing of 50.9% to Ahmadinejad, with official results suggesting that he has captured the support of 47.5% of those who cast their ballots for Reformist candidates in 2005. This, more than any other result, is highly implausible, and has been the subject of much debate in Iran.
Source:
The Iranian Guardian council has now admitted there was fraud in 50 cities. The Chatham House report shows that this fraud appears to be massive on a broad scale, not minor corruption that wouldn't change the election.
The effort by the Guardian council to minimize the extent of the fraud to just 3 million votes is not credible.
"Statistics provided by Mohsen Rezaei in which he claims more than 100% of those eligible have cast their ballot in 170 cities are not accurate -- the incident has happened in only 50 cities," Kadkhodaei said.
The spokesman, however, said that although the vote tally affected by such an irregularity is over 3 million, "it has yet to be determined whether the amount is decisive in the election results," reported Khabaronline.
In fact, preliminary analysis suggests by Chatham House suggests that some vote totals may have been computer generated, not counted. Further detailed analysis will be needed to verify that suspicion. However the totals were generated the massive shift of rural votes to Ahmadinejad from 2005 to 2009 is not credible because he was not popular with ethnic minorities in those rural areas .
Update:
Procedures for handling votes were changed in this election to the surprise of local rural election officials. Votes were not counted like they were in previous elections.
The proof was right in the village: "Interior Ministry officials came from Shiraz, sealed the ballot boxes, and took then away even before the end of voting at 9 pm," said Jalal. In all previous elections, a committee comprised of representative from each political faction had counted and certified the results right in the village. The unexpected change in procedures caught village monitors off guard, as it did everywhere else in the country.
It appears that Ahmadinejad's operatives knew he was losing so they changed the procedures for handling and counting the votes.