Rice (Oryza sativa) is the foremost cereal crop in Southeast Asia. It serves as staple food, thus has a major contribution to the calorie intake. In addition, rice contains melatonin which is beneficial for human health. It is, therefore, essential to retain this compound by appropriate rice production processes. Melatonin profile during rice production was monitored for three varieties (IR64, umbul-umbul and pandan wangi) from conventional farming and four varieties (batang lembang, pandan wangi, black and red rice) from organic farming. The effect of polishing degree on melatonin content in rice was also evaluated. Melatonin level decreased throughout rice production and then remained steady at roughly 25-40% in final product. The most influential factor was polishing which led to melatonin losses of up to 50%. The results for organically cultivated varieties were similar. However, melatonin in black rice appeared to be persistent in the matrix during rice production.