Previous studies in this laboratory have revealed the presence of substantial deposits of basic fibroblast growth factor (bFGF; FGF-2) in the myocardium from the earliest stages of heart development (Parlow et al. [1991] Dev. Biol. 146:139-147) and that an autocrine supply of bFGF is required for myocardial cell proliferation (Sugi et al. [1993] Dev, Biol, 157:28-37). Recently, an alternatively spliced isoform of bFGF, termed alt-bFGF, was described during later stages of embryogenesis, after heart morphogenesis is complete (Borja et al. [1993] Dev. Biol. 157:110-118). Because the antibody and nucleic acid probes used in our previous studies would have recognized canonical as well as alt-bFGF proteins and mRNAs, we have examined the expression of alt-and canonical bFGF mRNAs at early stages of embryogenesis, during which the initial differentiative and morphogenetic phases of heart development occur (Hamburger-Hamilton stages 3-24). Reverse transcription/polymerase chain reaction (RT/PCR) analysis detected the presence of both alt-bFGF and bFGF mRNAs in whole embryos as early as stage 3 and in the developing heart from the time of its initial appearance at stage 9. The presence of alt-bFGF mRNA was corroborated by RNase protection analysis which, in assessing RNA from whole embryos, revealed increasing levels of alt-bFGF mRNA between stages 5-18, suggesting that expression of alt-bFGF is developmentally regulated. Utilization of a probe that simultaneously protects segments of both alt- and canonical bFGF mRNAs indicated that alt-bFGF was the more abundant FGF isoform in the developing embryo until stage 24, when equivalent expression of each isoform was detected. Similar analysis revealed that alt-bFGF was the more abundant isoform in the embryonic heart, but that its relative expression was not decreased at stage 24.