Arising from below ground, the primary shoot is a straight, vertical axis bearing leaves in an opposite, decussate arrangement--an opposite pair at one node and the next pair, positioned 2.5 to 3.5 cm away, rotated 90 degrees.
The leaves of St. John's wort have no petioles. On the main (primary) stem, the blades are narrowly elliptic to narrowly lanceolate, less than 2.5 cm long and up to 1.0 cm wide, and smooth (entire) along the margins. Each blade has several prominent veins that diverge sharply from the midvein upward toward the leaf tip and dozens of translucent dots, the hypericin-producing glands. These, the largest leaves, are often pushed downward when the lateral shoots form, and the blade tends to be rolled upward (it is sometimes slightly involute).
A vertical ridge forms on the internode from the base of each leaf to the node below it, so that the stems have these diagnostic pairs of ridges, rotated 90 degrees from the pair above and below. Each node has a prominent ring around it. Neither the leaf nor the stem possesses any hairs (the plant is glabrous).
There is virtually no resting phase in the development of lateral shoots from the axillary buds of each node along the vertical stem. Lateral shoots grow at a very consistent angle (about 45 degrees), forming a plant body that looks like a truncated, four-sided obelisk.
Leaves along the lateral shoots are half the size of those on the primary shoot, and from their axillary buds form another order of lateral shoots that appear like tufts of very small leaves because the internodes of these shoots never elongate.
Flowers form in cymes on the top of the canopy, and often several flowers are open each day. Measuring 2.1 to 2.5 cm across, the flowers bear five golden-yellow petals with black dots (glands) and five green sepals. The petals are distinctly asymmetrical, irregularly serrated on either the left or the right side. Stamens are formed in three fascicles--two large (up to 28 stamens fused at their bases) and one smaller (about 20 stamens). The pistil has three widely spreading green styles. Sepals remain attached after the petals and stamens are lost, and the ovary develops into a capsular fruit that splits open along the partitions (a septicidal capsule).