Stem cells derived from umbilical cord tissue (UCT) and umbilical cord blood (UCB) in human subjects and horses can be obtained in a minimally invasive fashion with successful propagation of mesenchymal stem cells (MSCs). Currently there are no detailed protocols documenting a procedure to harvest UCB and UCT safely for equine stem cell propagation. UCB and UCT could be collected without harm to mare or foal. To develop a standard and safe method for UCB and UCT collection, and prospectively to compare foal and mare health between groups of animals where tissue was and was not collected. This study was conducted at a Thoroughbred breeding facility in central California in 2008. UCB and UCT were collected from 40 mare and foal pairs. Clinical parameters including time for foal to stand and nurse, time for mare to pass the placenta, and foal haematology data at age 24 h were documented and compared to a control group, consisting of the succeeding 40 mare and foal pairs. UCB was obtained successfully from 36 of 40 (90%) mares and UCT from 38 of 40 (95%) mares. Bacterial contamination was documented in 6 out of 36 (16.6%) UCB samples. There were no significant differences in time to stand or nurse for foals or time to pass the placenta for mares, between the experimental and control groups. There were no clinically relevant differences identified in haematological data obtained from foals with and without UCB collection. UCB and UCT can be harvested safely without harm to mares or foals. UCB and UCT samples collected in an inherently contaminated environment can be successfully disinfected and transported with minimal bacterial overgrowth for use in cell culture to isolate MSCs.