Alkaline phosphatase (ALP) in human choriocarcinoma cells (malignant trophoblasts) was characterized by its greater sensitivity to EDTA and l-leucine inhibition as compared with the placental isozyme. In addition, both the fully processed and the nonglycosylated forms of choriocarcinoma ALP migrated faster than the corresponding placental enzyme in sodium dodecyl sulfate-polyacrylamide gel electrophoresis. Choriocarcinoma cells express a 2.6-kilobase (kb) ALP mRNA unlike normal human placenta which expresses a 2.8-kb ALP mRNA. Administration of sodium butyrate to choriocarcinoma cells greatly increased the steady-state levels of the 2.6-kb choriocarcinoma ALP mRNA, which resulted in an increase in enzyme activity and biosynthesis. S1 nuclease analysis using probes derived from a placental ALP cDNA and ribonuclease protection assays employing probes derived from the germ cell ALP gene demonstrated that choriocarcinoma cells express the germ cell ALP gene. The germ cell ALP gene encodes the placental ALP-like isozyme that is primarily expressed in the thymus, testis, and germ cell tumors. The structures of the internal exons (II–X) of the germ cell ALP gene were determined previously based on their similarity to the placental ALP gene. However, the boundaries of exons I and XI (3′ exon) of the germ cell ALP gene were not defined due to sequence divergence between the two genes at the 5′ and 3′ regions. Ribonuclease protection and primer extension assays demonstrated that exon I of this gene is 119 base pairs in length and that germ cell ALP mRNA contains one major transcription initiation site. The isolation and characterization of germ cell ALP cDNA clones from a butyrate-treated choriocarcinoma cDNA library showed that the germ cell ALP mRNA is 2487 bases in length and exon XI of this gene is 1135 base pairs long.