This paper reports an investigation on optimal separation and detection for animal prostaglandins, i.e. prostaglandin E(2)(PGE(2)) and thromboxane B(2)(TXB(2)) by capillary zone electrophoresis with indirect detection at 254 nm. It was found that the addition of 3 mmol l(-1) phosphomolybdic acid in 5 mmol l(-1) chromate buffer can lower the detection limits of PGE(2) and TXB(2), i.e. the calculated detection limits (k=3) with phosphomolybdic acid is 0.05 mug ml(-1), only a 1/5-fold improvement compared to that without phosphomolybdic acid. Also adding phosphomolybdic acid, the mechanism for improving detection limits was explained properly. The separation and detection of PGE(2) and TXB(2) can be completed in 4 min. The linear ranges for PGE(2) and TXB(2) were the same, i.e. 5 approximately 80 mug ml(-1), analytical precision (n=8) was 1.2 approximately 1.4% and 3.5% for the measurement of migration times and determination of peak height, respectively. The approach was demonstrated in the lung tissue of SD rats, the measurement results were in good agreement with previous investigations.