Fifteen coffee samples comprising green, roasted, decaffeinated and instant coffees were analysed for their content of free and bound 3-chloropropane-1,2-diol (3-MCPD). Green coffees contained only traces of the free 3-MCPD. 3-MCPD in roasted coffees was found at the level of 10.1–18.5 µg/kg. The highest 3-MCPD level of 18.5 µg/kg was found in one instant coffee sample and in coffees with very long time application during roasting. The final colour of the roasted coffee beans was directly linked to the 3-MCPD formed, the darker beans having the greatest concentration, and arabica coffees contained lower 3-MCPD levels than robusta coffees. The level of bound 3-MCPD varied between 6 µg/kg (soluble coffees) and 390 µg/kg (decaffeinated coffee) and exceeded the free 3-MCPD level 8–33 times. Arabica coffees contained higher levels of the bound 3-MCPD than robusta coffees. The recognised precursors of 3-MCPD (salt, glycerol, lipids) were also determined and their influence on the formation of the free and bound 3-MCPD was discussed.