Intercross of mice transgenic for Flp-recombinase with the CD19cre mouse strain leads to excision of the Frt-flanked neo (R) cassette from the CD19cre knock-in transgene. This significantly reduces the expression level of Cre by the CD19cre transgene and consequently decreases the extent of Cre-mediated recombination of loxP-flanked alleles, most likely due to the fact that this neo (R) cassette contains polyoma enhancer sequences. We wish to draw attention to this finding, since the Flp-deleter mouse strain is commonly used to remove Frt-flanked selection cassettes in vivo from conditional alleles. Therefore conditional alleles have to be separated from the Flp-deleter transgene by breeding before crosses with CD19cre mice are initiated. In addition our findings suggest that gene expression from the CD19 locus can be increased by the insertion of exogenous enhancer sequences, without compromising B cell specificity.