We designed a new semi-quantitative competitor-based PCR assay to assess the amount of p190 BCR-ABL mRNA in patients with Ph-positive ALL. Transcript numbers were compared in 29 paired specimens of blood and marrow collected contemporaneously from 18 patients at differing stages of disease. In general, the numbers of BCR-ABL transcripts detected in marrow in blood were not significantly different (p = 0.1). However, in four samples BCR-ABL transcripts (< 10-1000/micrograms RNA) were detected in the marrow while the blood was negative; the reverse, positive blood and negative marrow, was not seen. In a further three samples the number of BCR-ABL transcripts was more than 10-fold higher in the marrow. We measured the number of ABL transcripts/micrograms RNA in all samples as an internal standard in order to control for variations in sample quality and other parameters. For two out of the four discordant samples in which blood was PCR negative, the number of ABL transcripts/micrograms RNA detected in the marrow was substantially higher than in the blood, suggesting poor quality blood specimens. However, the ratio of BCR-ABL to ABL in marrow and blood was similar for the three discordant samples in which both tissues were PCR positive. We conclude that in general, blood and marrow contain similar BCR-ABL transcript numbers in Ph-positive ALL but some samples are discordant. Marrow is therefore the preferred tissue for residual disease studies. Quantification of ABL mRNA as an internal control is useful in the interpretation of competitive PCR data and may serve as a robust way to standardize results between laboratories.