A detailed electron microprobe (EMP) and laser-ablation inductively coupled plasma mass spectrometry (LA-ICP-MS) study of zircon from six types of miaskitic and agpaitic alkaline pegmatite from the Larvik Plutonic Complex, Oslo rift valley, Norway, was undertaken to shed light on the pegmatite petrogenesis. Detailed rare earth element (REE) analyses indicate important differences between the zircon from each type of pegmatite. Primary zircon from miaskitic Stavern-, Tvedalen- and Stålaker-type pegmatites has a mean ΣREE = 704 ppm, is depleted in LREE and has a significant positive Ce anomaly (Ce/Ce* = 44–67) and negative Eu anomaly (Eu/Eu* = 0.15–0.18). Secondary Tvedalen-type zircon is REE-enriched (ΣREE = 5035 ppm), with a flatter REE pattern, Ce/Ce* = 0.97 and a Eu anomaly similar to primary Tvedalen-type zircon (Eu/Eu* = 0.21). Secondary zircon from agpaitic Langesundsfjord-type pegmatites display a distinctive flat REE pattern characterized by overall REE enrichment (ΣREE = 967), Ce/Ce* = 1.92, and a minor negative Eu anomaly (Eu/Eu* = 0.37). Zircon from agpaitic Bratthagen-type pegmatites occurs as both altered primary and secondary phases and is strongly enriched in REE relative to other zircon (ΣREE = 4178 and 8388, respectively). Primary Bratthagen-type zircon has a similar REE pattern to miaskitic zircon, with a steeper HREE profile and smaller Ce and Eu anomalies (Eu/Eu* = 0.73; Ce/Ce* = 6.22). Secondary Bratthagen-type zircon is strongly enriched in LREE compared to primary zircon, does not display a positive Ce anomaly and has Eu/Eu* = 0.56. The altered primary and secondary Bratthagen-type zircons have elevated Th/UN ratios, suggesting a different melt source for Bratthagen-type agpaitic pegmatites. Zircon from external pegmatites has trace-element signatures similar to Stavern-, Tvedalen- and Stålaker-type primary zircon with Ce/Ce* = 214 and Nb/Ta and Th/U ratios that are similar to those of secondary Langesundsfjord- and Bratthagen-type zircon. It is suggested that the parental melt of the external pegmatites is the same as the miaskitic pegmatites, but that it has undergone alteration by hydrothermal fluids derived from the host basalt, or by post-magmatic F-rich fluids which mobilize Nb and Th. On the basis of texture, morphology and geochemistry, two populations of zircon can be recognized: (1) primary zircon from miaskitic pegmatites; and (2) secondary zircon from post-magmatic, hydrothermal assemblages. The U–Th–Pb isotope analyses indicate that the secondary and altered zircon are depleted in 238U, and enriched in LREE. Interaction of a post-magmatic hydrothermal fluid with an externally derived meteoric fluid is suggested to have influenced the REE signatures, and in particular the Eu and Ce anomalies of the late-stage zircons.