Background: There is an ongoing debate as to whether the outcome of ICSI is affected by the origin of sperm used or by the severity of male factor infertility. Methods: Data from a multicentric prospective, controlled cohort study in Germany were analysed to look for differences in pregnancy course and outcome following the use of either ejaculated, epididymal or testicular sperm. Pregnancies were recruited before the 16th week of gestation and included only when they were still ongoing in the 16th week of gestation. A total of 2809 pregnancies was originally included in the study. For 2545 pregnancies with 3199 fetuses/children, data of sperm count and origin were available. Results: Regarding pregnancy course and complications, there was no influence of the origin of sperm. No higher risk of pre-eclampsia was associated with the use of surgically obtained sperm. The birth data of children were similar between the three groups (ejaculated, epididymal, testicular sperm). The risk of major malformation in abortions, stillbirths, livebirths and induced abortions was not significantly different between the three groups, but these results must be treated with caution because of the low numbers in some groups. Major malformation rates did not depend on the number of sperm in the ejaculate. Conclusions: The course of pregnancy as well as the outcome after ICSI is neither affected by the origin of sperm nor by the number of sperm in the ejaculate.