Our aim was to study the antibiotic prescription practices and the knowledge about antibiotic costs, brand and generic drugs of paediatricians working in two hospitals in Greece. The 2007 national guidelines were used as the gold standard for antibiotic prescription. A total of 126 paediatricians participated in the study (50.4% response rate). The mean compliance rate with the guidelines was 50.1% (range per infection: 10.6-84.7%). The mean scores of knowledge about antibiotic costs and about brand name and generic drugs were 35.6 and 60.3%, respectively. Linear regression analysis found a significant association between the mean compliance rate with the national guidelines and the paediatricians' age (mean compliance rates were 49.1, 53.0, and 43.0% in the ≤ 30, 31-40, and > 40 years age-groups, respectively; P  =  0.003). In conclusion, five years after the first national guidelines were issued in Greece only half of the paediatricians working in hospitals comply fully with them.