Although the application of tolls and vignettes is not mandatory for Member States, the Directive lays down certain rules to be followed by those Member States if they wish to levy those charges. The most important of these framework conditions are:
- Tolls must be levied according to the distance travelled and the type of vehicle; vignettes are scaled according to the duration of the use made of the infrastructure and to the vehicle's emission class;
- The directive does not permit to impose tolls and vignettes at the same time for the use of a single road section. Only as an exception tolls can be levied for the use of bridges, tunnels and mountain passes on networks where vignettes are applied;
- National tolls and vignettes must be non-discriminatory, excessive rebates on tolls are forbidden;
- Charging schemes should cause as little hindrance as possible to the free flow of traffic, avoiding mandatory checks at the EU’s internal borders;
- The Directive also stipulates that the maximum average tolls must be set in relation to the costs of constructing, operating and developing the infrastructure concerned. New tolling schemes must be notified.
- Tolls may also include an "external cost charge" which reflect the cost of air pollution and of noise pollution provided that the external cost charges respect maximum values defined in the annexe of the Directive.
- The revenue should be used for preferably to develop the trans-European network
A specific provision of the directive allows Member States to co-operate for the purpose of introducing a common system of electronic vignettes. In this respect Belgium, Denmark, Luxembourg, the Netherlands and Sweden have a common system of user charges for heavy goods vehicles above 12 tonnes called the 'Eurovignette' system . This system allows hauliers after the payment of a specified amount to use motorways of the participating Member States for a given period (i.e. a day, a week, a month or a year). Each participating country is responsible for all aspects related to the payment of the Eurovignette on its own territory.
The internalisation of the external costs of road transport is also subject to the Directive 2011/76/EU amending Directive 1999/62/EC on the charging of heavy goods vehicles for the use of certain infrastructures.