Inhale. Exhale. Although respiration differs in each main reptile group, all reptiles breathe air through the use of lungs. Despite lacking a diaphragm muscle, reptiles have a diaphragm-type respiratory system and the act of breathing is accomplished by the reptile moving its throat or rib cage. Air flow through the lungs is bidirectional, air travels into the lungs through the bronchial tubes to tiny air sacs, or alveoli. The exchange of oxygen and carbon dioxide takes place within the alveoli and the used air is then exhaled out of the lungs through the same route which it enterred.
The act of breathing can be quite a task for some reptiles due to there body and lung structure. The lungs of squamates (lizards and snakes) are ventilated by the axial musculature. These same muscles are used for locomotion so most squamates are forced to hold their breath while running. Some lizards work around this by completely filling their lungs by buccal pumpling which allows them to remain aerobically acitve for a longer period of time.
Eating for many reptiles can make breathing a challenge as most reptiles lack a secondary palate and must hold their breath while swallowing. Some species have adapted a different approach to eating. Snakes for example can extend their trachea allowing them to swallow large prey without suffering from asphyxiation, while crocodilians have developed a secondary palate which allows them to continue breathing while remaining submerged.
Turtles and tortoises have the biggest challenge in breathing due to their rigid shell which doesn't allow for the expansion and contraction used to ventilate the lungs. Many turtles and tortoises have found a solution to this problem. The lungs of a turtle are attached to the inside of the carapace with the bottom of the lungs attached to the viscera. Turtles achieve effective respiration by moving the viscera up and down using a series of muscles equivalent to a diaphragm. During locomotion, some turtles hold their breath the breathe in bouts as they rest, while others breathe continuously during locomotion by taking small pauses for breath between bouts of locomotion.
Some species have developed more permeable skin, such as aquatic turtles, or have modified their cloaca to increase the area for gas exchange. Breathing, despite the various adaptations reptiles have made over time, can not be fully accomplished without the use of lungs.