The motivation to create Free Economic Zones in Republic of Moldova appeared in 1990-1993. This idea was much older, but remains in the offices of the new leadership of the newly independent state, and at 25 May 1993 was adopted the first law no.1451-XII regarding Free Enterprise Zones. With the adoption of this law, has laid the foundation work of Free Economic Zones in Moldova. Later this law was replaced by the Law of Free Economic Zones nr. 440-XV from 27.07.2001, which is currently in force. Changes in legislation have occurred as a result of experience gained by the residents of Free Economic Zones. Facilities and restrictions provided for FEZ were divided in several parts: customs, fiscal and commercial. Each category represents a special regulation, in parallel with common right, which continues to be applied, in its own integrity, in the rest of the territory, namely customs zones. The purpose of this study is to develop the "customs regime", barriers and trends observed in particularity by residents of Free Economic Zones. They refer to the system of obligatory customs declaration of goods (services) imported and exported from this zones; regime of circulation of goods (services) between residents of Free Economic Zones, procedure of supervision waste processing; prohibiting of import in free zones of goods and other objects, which are forbidden by law of Republic of Moldova or/and international agreements; presentation to Customs Service of reports by residents of free zones, which describe the flow of materials and finished goods.