This study aims to compare the efficiency of the automated system (controlled-rate freezer) and the conventional system (manual system) for freezing the equine semen after cooling at 16o C. The parameters evaluated were: motility, strength, plasmatic and acrosomal membrane integrity of spermatozoa from twelve stallions. Ejaculates from stallions were collected three times per week, during four weeks. Gelfree semen was diluted in skim milk extender and cooled at 16ºC for 24 h. After cooling, extended semen was centrifuged at 600 x g for 10 min. The supernatant was removed and sperm pellets were re-suspended using the freezing extender. Samples were then packed into 0.5 ml straws, which were divided into two parts: one for cryopreservation in a controlled-rate freezer (CR) and the other for a manual system (MS). In this study, CR showed higher values for motility (44.6%), viability (57.9%) and plasmatic membrane integrity (29.3%) when compared with MS (20, 35.7 and 5.1%), (P < 0.05), respectively, after 24 h of cooling at 16ºC. The automated system for cryopreservation of cooled semen at 16°C for 24 h was more efficient, with higher values of motility, viability and plasmatic membrane integrity when compared with the manual system.