It was bound to happen sooner or later: Google’s search engine, which has a market share of between 80% and 90% in Europe faces its first major antitrust challenge. Late Tuesday, the European Commission asked Google to respond to complaints lodged by three other search engines: Foundem, Ciao, and Ejustice.fr. Not surprisingly, one of those companies, Ciao, is owned by Microsoft. As the Telegraph points out: “the bigger picture here is the battle between the two multi-billion pound internet giants for web supremacy.”

The details are not so complex: Foundem claims Google was rigging its algorithms to give competing search engines short shrift in the rankings. Google, predictably, says no way, before playing the sympathy card:

We are also the first to admit that our search is not perfect, but it’s a very hard computer science problem to crack. Imagine having to rank the 272 million possible results for a popular query like the iPod on a 14 by 12 screen computer screen in just a few milliseconds. It’s a challenge we face millions of times each day.

On tech issues, the EU’s Competition Commission is famously hard to predict: during the Mario Monti years it nailed Microsoft, forcing it to cleave off Internet Explorer from Windows, but then it let the Google-DoubleClick deal through with little fuss while Neelie Kroes was in charge there. The new man of the hour at the Commission is Joaquín Almunia Amann.

Will he do a better job of understanding Google’s complex search algorithm in meting out justice? Let’s hope so. An EC judgment on the this matter could do more to affect digital commerce and advertising than any of the preceding cases.