Analysis of serial cross-sections of the Chlamydomonas flagellum reveals several structural asymmetries in the axoneme. One doublet lacks the outer dynein arm, has a beak-like projection in its B-tubule, and bears a two-part bridge that extends from the A-tubule of this doublet to the B-tubule of the adjacent doublet. The two doublets directly opposite the doublet lacking the arm have beak-like projections in their B-tubules. These asymmetries always occur in the same doublets from section to section, indicating that certain doublets have consistent morphological specializations. These unique doublets give the axoneme an inherent structural polarity. All three specializations are present in the proximal portion of the axoneme; based on their frequency in random cross-sections of isolated axonemes, the two-part bridge and the beak-like projections are present in the proximal one quarter and one half of the axoneme, respectively, and the outer arm is absent from the one doublet greater than 90% of the axoneme's length. The outer arm-less doublet of each flagellum faces the other flagellum, indicating that each axoneme has the same rotational orientation relative to the direction of its effective stroke. This strongly suggests that the direction of the effective stroke is controlled by a structural component within the axoneme. The striated fibers are associated with specific triplets in a manner suggesting that they play a role in setting up or maintaining the 180 degrees rotational symmetry of the two flagella.