Coxiella burnetii is the causative agent of the zoonotic disease Q fever. Since its first recognition as a disease in the 1930s, the knowledge about the agent and the disease itself has increased. This review summarizes the current knowledge on C. burnetii and Q fever, its pathogenesis, diagnosis and control. C. burnetii is a bacterium which naturally replicates inside human or animal host cells. The clinical presentation of Q fever varies per host species. C. burnetii infection in animals is mainly asymptomatic except for pregnant ruminants in which abortions and stillbirth can occur. In humans, the disease is also mainly asymptomatic, but clinical presentations include acute and chronic Q fever and the post-Q fever fatigue syndrome. Knowledge of the pathogenesis of Q fever in animals and excretion of C. burnetii in infected animals is crucial in understanding the transmission routes and risks of human infection. Our studies indicated that infected pregnant animals only excrete C. burnetii during and after parturition, independent of abortion, and that C. burnetii phase specific serology can be a useful tool in the early detection of infection. Domestic ruminants are the main reservoir for human Q fever, which has a major public health impact when outbreaks occur. In outbreaks, epidemiological source identification can only be refined by genotypic analysis of the strains involved. To control outbreaks and Q fever in domestic ruminants, vaccination with a phase 1 vaccine is effective. Future challenges are to identify factors for virulence, host susceptibility and protection.