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A cross-sectional survey of 1216 newly pregnant women (mean age = 31 years) from 32 general practices and five family planning clinics was conducted to find the prevalence of chlamydial infection and to evaluate self-administered vaginal swabs and first-pass urines for detection of Chlamydia trachomatis by ligase chain reaction assay. Overall prevalence of infection was 2.4% (95% CI = 1.5 to 3.3) but in women aged less than 25 years it was 8.6% (95% CI = 4.1 to 12.9) and in pregnant teenagers it was 14.3% (95% CI = 3.7 to 24.9). In 1161 women with both swab and urine results, 25 women were positive on both specimens three on swab alone, and one on urine alone. When asked which they preferred to provide, 47% said urine, 59 swab and 48% preferred both equally. This is the first study to show that non-invasive screening in early pregnancy is feasible in the community. Although swabs detected 10% more infections, nearly half the women preferred providing urine specimens.