The purpose of the present study was to evaluate the safety of MicroSort (MicroSort Division, GIVF, Fairfax, VA, USA) sperm sorting by monitoring major malformations in infants and fetuses conceived using sorted spermatozoa. Data were collected in a prospective protocol with monitoring that began from conception through birth until 1 year of life. Comprehensive ascertainment identified fetuses and stillbirths with malformations after 16 weeks gestation, pregnancies terminated for malformations and babies with major malformations. Outcomes in MicroSort pregnancies were compared with outcomes in published studies that used active and comprehensive ascertainment of malformations in the general population and in pregnancies established after assisted reproduction. Using comprehensive outcomes from all pregnancies, the rate of major malformations in MicroSort pregnancies conceived after IVF with or without intracytoplasmic sperm injection was 7.8%; this did not differ significantly from the rates reported in the three assisted reproductive technology control studies not associated with MicroSort (8.6%, 9.2% and 8.3%). Similarly, the rate of major malformations in MicroSort pregnancies initiated with intrauterine insemination was 6.0%, not significantly different from that reported in non-assisted reproductive technology pregnancies not associated with MicroSort (6.9%, 4.6% and 5.7%). Prospective record review of pregnancy outcomes and paediatric evaluation to 1 year indicate no association between MicroSort sperm sorting and major malformations.