Forty-eight young adult New Zealand albino rabbits were entrained to a daily 12-hr light and 12-hr dark cycle. Under a constant dark environment, rabbits were sacrificed at 4-hr intervals, beginning at 2 hr before the accustomed lights-on period. Eight rabbits were used for each of the 6 time points within 24 hr. Aqueous humor and vitreous humor samples were collected. Samples from one eye of each rabbit were assayed for prostaglandins D2, E2, and F2alpha by enzyme immunoassay. Total protein concentrations in the samples were also determined. Concentrations of prostaglandins D2 and F2alpha in the aqueous humor were found to vary in a consistent pattern. The prostaglandin F2alpha concentration increased in the early subjective light period, remained high in this period, and decreased in the subjective dark period. The prostaglandin D2 concentration was elevated only in the early subjective light period. No significant change of aqueous humor prostaglandin E2 level was found. Total protein concentration in the aqueous humor varied in a similar pattern as the aqueous humor prostaglandin F2alpha, indicating a close association between the permeability of protein across the blood-aqueous barrier and the endogenous prostaglandin F2alpha level. In the vitreous humor, concentrations of all three prostaglandin subtypes remained unchanged, as did the total protein concentration. However, vitreous humor concentrations of prostaglandin D2 and F2alpha were significantly higher than their concentrations in the aqueous humor.