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Background Group B streptococcus (GBS) is a leading cause of severe infections in newborns. Intrapartum antibiotic chemoprophylaxis (IAP) reduces the rate of early-onset disease. The aim of this study is to determine the degree of clinicians’ compliance with the suggested protocol for GBS prevention in Emilia-Romagna (Italy). Methods Characteristics of each delivery were prospectively recorded in the period between October 2005 to December 2005. Standardized proforma were used to collect data. Results Among 5118 babies, 7.2% (369) were preterm and 92.3% were born at term (4749). Antenatal screening was performed in 86.6% of women who delivered at term, of which 18.1% were GBS culture-positive. Information regarding culture site was available in 93.2% of women screened and recto-vaginal cultures were documented in 42.7%. IAP was administered to 28.7% of 3937 women at term who had either spontaneous delivery or emergency caesarean section. In this cohort, 15.9% were diagnosed GBS culture-positive, of which 92.6% received IAP. Prophylaxis was also administered to 8.4% (331) of women for no apparent reason. Compared with tertiary level hospitals, women delivering in primary/secondary hospitals were more likely to be both GBS screened ( P < 0.0001; OR 3.04; CI 2.33-3.97) and to receive prophylaxis ≥4 hours before delivery ( P = 0.0025; OR 1.57; CI 1.17-2.12). Conclusions GBS screening was performed in > 85% of women and > 90% of culture-positive women received prophylaxis. However, there is a need to educate clinicians about protocol adherence, as most cultures were suboptimal and cases of unnecessary IAP were administered. The screening was more effective in hospitals with fewer deliveries.