An HPLC method for the simultaneous determination of paraquat and diquat in aqueous solutions and biological fluids (plasma, urine and vitreous humour) was developed. This method is based on the initial ion-pair solvent extraction of both herbicides from plasma or urine. Vitreous humour samples required a protein precipitation and concentration process. Relatively small sample volumes (1 mL of plasma or urine, and 100 μL of vitreous humour) were enough to determine paraquat and diquat by the proposed technique. Chromatography was carried out using a LiChrospher(r)100 RP-18 (5 μm) column for aqueous solutions and plasma and urine extracts, or a Nova-Pak C18(3.9 × 150 mm) column for vitreous humour extracts. Two ultraviolet wavelengths were selected, 254 nm for paraquat and 310 nm for diquat. The calibration curves were linear in the concentration ranges 0.42–8.4 μg/mL for aqueous solutions, 0.1–2 μg/mL for plasma, 0.1–3 μg/mL for urine and 0.5–5 μg/mL for vitreous humour.