Data about the effectiveness of different antibiotic regimens for the treatment of acute Q fever from clinical studies is scarce. We analysed the antibiotic treatment regimens of acute Q fever patients in 2007 and 2008 in The Netherlands and assessed whether hospitalization after a minimum of 2 days antibiotic therapy was related to the initial antibiotic therapy. Clinical data on antibiotic treatment and risk factors of acute Q fever patients were obtained from general practitioner medical records and self-reported by patients. For the 438 study patients, doxycycline was the most commonly prescribed initial antibiotic in both study years. After adjustments for confounding factors, doxycycline (200 mg/day), moxifloxacin, as well as other possibly effective antibiotics [including other new fluoroquinolones and doxycycline (100 mg/day)] showed significant lower risks for hospitalization compared to β-lactam antibiotics and azithromycin (reference group), with the lowest risk for doxycycline (200 mg/day) (odds ratio 0·04, 95% confidence interval 0·01–0·22). These data support current guidelines that recommend doxycycline as the first choice antibiotic for treating acute Q fever.