A method of processing sperm cells comprising the steps of: providing a semen sample containing sperm cells collected from a male animal; transporting the semen sample containing sperm cells collected from a male mammal to a sperm processing facility; conducting an initial quality control check on the semen; staining the sperm cells in said semen sample with a DNA selective fluorescent dye that selectively binds to DNA in the sperm cells by exposing said sperm cells to a DNA selective fluorescent dye to form a staining mixture, and subjecting the staining mixture to a temperature of at least 40°C; using a flow cytometer to sort the sperm cells on the basis of a specified DNA characteristic; obtaining a quantity of sperm cells having a desired DNA characteristic suspended in a volume of fluid; and adjusting the concentration of sperm cells in said suspension by performing a concentration process to achieve a desired concentration; and cooling said quantity of sperm cells from a temperature that exceeds 20°C to a temperature in the range of 0-8°C, and adding a protein source and cryoprotectant to said sperm cells before the temperature of the sperm cells has been cooled below 20°C, wherein cooling comprises using a programmable freezer to: (a) cool the sperm cells to a holding temperature in the range of 0-8°C; (b) maintain the sperm at said holding temperature for a period of less than 60 minutes to allow the sperm cells to equilibrate with the cryoprotectant; (c) cool the sperm at a first cooling rate to a temperature that approaches a critical temperature zone in which ice crystal formation and changes in osmotic pressure damage sperm cells; and (d) cool the sperm cells through said critical temperature zone at a second cooling rate faster than said first cooling rate. providing a semen sample containing sperm cells collected from a male animal; transporting the semen sample containing sperm cells collected from a male mammal to a sperm processing facility; conducting an initial quality control check on the semen; staining the sperm cells in said semen sample with a DNA selective fluorescent dye that selectively binds to DNA in the sperm cells by exposing said sperm cells to a DNA selective fluorescent dye to form a staining mixture, and subjecting the staining mixture to a temperature of at least 40°C; using a flow cytometer to sort the sperm cells on the basis of a specified DNA characteristic; obtaining a quantity of sperm cells having a desired DNA characteristic suspended in a volume of fluid; and adjusting the concentration of sperm cells in said suspension by performing a concentration process to achieve a desired concentration; and cooling said quantity of sperm cells from a temperature that exceeds 20°C to a temperature in the range of 0-8°C, and adding a protein source and cryoprotectant to said sperm cells before the temperature of the sperm cells has been cooled below 20°C, wherein cooling comprises using a programmable freezer to: (a) cool the sperm cells to a holding temperature in the range of 0-8°C; (b) maintain the sperm at said holding temperature for a period of less than 60 minutes to allow the sperm cells to equilibrate with the cryoprotectant; (c) cool the sperm at a first cooling rate to a temperature that approaches a critical temperature zone in which ice crystal formation and changes in osmotic pressure damage sperm cells; and (d) cool the sperm cells through said critical temperature zone at a second cooling rate faster than said first cooling rate. (a) cool the sperm cells to a holding temperature in the range of 0-8°C; (b) maintain the sperm at said holding temperature for a period of less than 60 minutes to allow the sperm cells to equilibrate with the cryoprotectant; (c) cool the sperm at a first cooling rate to a temperature that approaches a critical temperature zone in which ice crystal formation and changes in osmotic pressure damage sperm cells; and (d) cool the sperm cells through said critical temperature zone at a second cooling rate faster than said first cooling rate.