This study was designed to establish if ultrasound could detect differences in uterine zonal anatomy between conception and non-conception in-vitro fertilization (IVF)/embryo transfer cycles. A transvaginal ultrasound scan was performed on the day of down regulation (D0), on day 8 of ovulation induction (D8), on the day of human chorionic gonadotrophin (HCG) injection, at the time of oocyte retrieval, and at embryo transfer. Thicknesses of endometrium, junctional zone, myometrium and full thickness of the uterus were recorded for every patient and comparisons made at all the assessment points. Differences between measurements on D0 and all other measurements (temporal changes) and between every subsequent measurement (dynamic changes) were also compared. There were no statistically significant differences in endometrial thickness between pregnant and non-pregnant groups at any time. The diameter of the uterus increased during therapy and was significantly greater in the pregnant subset at the time of HCG injection, oocyte retrieval and embryo transfer (P < 0.02, 0.03 and 0.02 respectively). The myometrium was significantly thicker in the pregnant group on D0, on D8 and at HCG administration (P < 0.03, 0.004 and 0.02). There was a decrease in junctional zone thickness in both groups during the first week of ovulation induction, and on D8 the junctional zone in pregnant patients was significantly thinner (P < 0.04). The junctional zone became significantly thicker at embryo transfer in the pregnant group (P < 0.01). This was confirmed by significant temporal and dynamic changes at the time of oocyte retrieval and embryo transfer (P < 0.01, 0.0001 and P < 0.05, 0.01 respectively). In the patients who did not conceive, changes in the junctional zone were less pronounced. In conclusion, it was not possible to predict the likelihood of pregnancy from endometrial thickness at any time during the IVF cycle, but changes occurred in other uterine layers that were more pronounced in conception cycles. The responsiveness of the junctional zone seems to be associated with implantation, and its measurements at the time of downregulation and embryo transfer can be used to predict treatment outcome.