Holder did not say why he believed the original judge was biased, only declaring in court papers that he and his clients "believe that they cannot have a fair and impartial trial or hearing" in Connelly's court. California law allows either side in Superior Court cases to make one peremptory challenge to disqualify a judge without giving a reason.

Holder's office did not respond to an inquiry about the judge, instead referring questions to Raudabaugh, who said only that a review of his past case rulings made her organization and the other plaintiffs uncomfortable with him.

Connelly was to have held a hearing next month on a request for a preliminary injunction against the rail authority. That hearing has been canceled, and the case has been transferred to a different judge within the Sacramento Superior Court -- the same judge scheduled to hear Chowchilla's high-speed rail lawsuit.

Each of the pending cases takes a different approach in attacking the high-speed train plans.

The rail authority is planning a 520-mile line to connect San Francisco to Los Angeles and Anaheim, by way of the San Joaquin Valley, with trains capable of traveling up to 220 mph. The Merced-Fresno section is the first portion for which the agency has certified a final environmental impact report and approved a route.

The federal government has committed about $3.3 billion in stimulus and transportation money to start construction on a stretch between Madera and Bakersfield. But that money will evaporate if the Legislature does not agree to put up $2.7 billion from Proposition 1A, a bond measure approved by voters in 2008.

The suit by Madera County and the two farm bureaus focuses largely on claims that the rail authority's Merced-Fresno EIR did not adequately assess the effects on agriculture of building and operating the train system, nor does it provide sufficient measures to make up for those effects.

Chowchilla's lawsuit argues that the EIR failed to address "the impacts of splitting the city of Chowchilla in half by routing" tracks along Highway 99. The suit also claims that the authority failed to evaluate effects of the trains and the route on traffic, noise and public safety transportation routes "as was done for the city of Madera."

While the authority approved a route for the train between Merced and Fresno, it left undecided how and where the trains would run through or around Chowchilla, where tracks would branch off to head west toward Gilroy and San Jose. That connection is being deferred until the authority completes work on an environmental assessment of the San Jose-Merced section.

The Chowchilla suit asserts that by approving a Merced-Fresno route, however, the authority has limited the potential for a full environmental analysis of various options for the San Jose connection and violated the California Environmental Quality Act.

The third lawsuit was filed by Thornton on behalf of Timeless Investments LLC, Millennium Acquisitions, Horizon Enterprises and Everspring Alliance, each of which owns land that would be affected by the rail line.

Thornton said Timeless and Millennium own property along Golden State Boulevard in northwest Fresno, including the former Klein's Truck Stop. Everspring owns a 136-acre parcel of farmland at Avenue 12 and Road 30 1/2 in Madera County. The route approved by the authority last month would go through both the farmland and the Klein's site.

Horizon also owns properties that could be in the path of the tracks, depending on the route.

The suit complains that the Merced-Fresno EIR is a failure because it does not consider alternative routes that might cause less environmental harm or disruption to agriculture or businesses. Those options include the Interstate 5 freeway corridor on the Valley's west side and routes that run through largely vacant property in northwest Fresno between the San Joaquin River and Bullard Avenue.

In court papers, Thornton also alleges that the rail authority virtually ignored modern high-speed-train technology that he said could allow a main train line to run along the I-5 corridor with branches into Valley cities. "The authority has simply failed to include modern technology when determining whether a trunk-and-branch system will reduce an impact on the environment," Thornton said in court papers.

Like the Madera County and Chowchilla cases, Thornton's case will be heard in Sacramento Superior Court. It has been assigned to Connelly -- the judge who was disqualified from hearing the Madera County lawsuit.