Group B streptococcus (GBS) is an important aetiological agent of serious neonatal infections. A rapid and sensitive method for the detection of GBS colonization in pregnant women at delivery could make intrapartum screening for GBS possible. A real-time PCR method targeting the sip gene of GBS in pregnant women at delivery has been evaluated. The performance of the real-time PCR was compared with optimized GBS culture. Separate vaginal and rectal swabs were collected from women hospitalized at the delivery department at St Olavs Hospital, Trondheim, Norway, from January 15 through May 2005. The specimens were cultured on selective blood agar plates and in selective broth and examined by real-time PCR. Of samples from 251 women, 87 (34.7 %) were GBS positive by culture and 86 (34.3 %) were positive by PCR. Using GBS culture as the ‘gold standard’, the sensitivity of real-time PCR was 0.97 (95 % confidence interval 0.90–0.99) and specificity was 0.99 (95 % confidence interval 0.97–1.00). In two women the PCR was positive and the culture negative. Additional analysis using cylE PCR substantiates that these two women were true GBS carriers with negative GBS culture. The rate of GBS colonization was lower in vaginal specimens than in rectal specimens both by culture and PCR. The real-time PCR assay is fast, highly sensitive and specific for detecting GBS colonization in pregnant women at delivery, and has the potential for intrapartum detection of GBS colonization. Both vaginal and rectal samples are required to achieve highest possible detection rate.