The Trouble with Atheism is an hour-long documentary on atheism, presented by Rod Liddle. It aired on Channel 4 in December 2006. The documentary focuses on criticizing atheism, as well as science, for its perceived similarities to religion, as well as arrogance and intolerance. The programme includes interviews with a number of prominent scientists, including atheists Richard Dawkins and Peter Atkins and Anglican priest John Polkinghorne. It also includes an interview with Ellen Johnson, the president of American Atheists.

Liddle begins the documentary by surveying common criticisms of religion, and particularly antireligious arguments based on the prevalence of religious violence. He argues that the “very stupid human craving for certainty and justification”, not religion, is to blame for this violence, and that atheism is becoming just as dogmatic as religion. In order to support his thesis, Liddle presents numerous examples of actions and words by atheists which he argues are direct parallels of religious attitudes. He characterizes Atkins and Dawkins as “fundamentalist atheists” and “evangelists”.

In response to atheistic appeals to science as a superior method for understanding the world than religion, Liddle argues that science itself is akin to religion: “the problem for atheists is that science may not be as far away from religion as you might imagine”. He describes Fermilab, a U.S. Department of Energy National Laboratory focused on particle physics, as a “temple to science”, and characterizes Charles Darwin’s The Origin of Species as a “sacred text” for atheists.