Clean Energy Fuels (Nasdaq: CLNE) founder T. Boone Pickens' vision of a country run on natural gas is taking slow steps forward, but it may not be enough for anxious investors.

Revenue was up an impressive 46% in the third quarter to $45.7 million, despite gasoline gallon equivalents delivered only increasing from 29.5 million to 31.3 million. On a non-GAAP basis, net loss fell to $1.8 million, but there was a $7.9 million non-cash gain related to Series I Warrants skewing numbers positively.

What we should really be watching is adjusted EBITDA, which eliminates these non-cash charges. This is where Clean Energy is looking a little ragged this quarter; adjusted EBITDA fell to a loss of $568,830 from a gain of nearly $5.4 million in 2009.

But there were a few positive developments in the quarter that could point to brighter days at Clean Energy. Los Angeles just signed a 10-year contract to service fueling facilities for four agency divisions consisting of 2,500 buses. The deal is anticipated to be for around 40 million gallons of compressed natural gas annually.

Clean Energy is also partnering with Pilot Flying J to build natural gas truck fueling facilities throughout the US. These 550 locations could help unlock the trucking market for natural gas as manufacturers start to roll natural gas trucks off the assembly lines for 2010. Pilot Flying J gives natural gas a starting foothold to compete against big oil companies like ExxonMobil (NYSE: XOM) and Chevron (NYSE: CVX) without being a separate destination.

The new agreements help bring natural gas to a wider market, but Clean Energy is having a tough time showing a profit despite the revenue growth. Investors would be wise to wait for Clean Energy to show some real profit before getting excited about this stock.

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Fool contributor Travis Hoium does not have a position in any company mentioned. You can follow Travis on Twitter at @FlushDrawFool, check out his personal stock holdings or follow his CAPS picks at TMFFlushDraw.

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